Computational Chemistry

Computational Chemistry

  • Ali Shokuhi Rad added an answer:
    How to use split Basis Sets for different atoms
    I'm doing a part-time calculation using Gaussian DFT method. My molecules contain C, H, N, P and Pt (Au/Ru sometime). I read some papers, they use split basis set for this kind of molecule, and very often they use LANL2DZ for Pt and 6-31G* for C, H, N and P.
    So i have 2 questions regarding this matter, please help me!
    1- How important it is to use split basis set? Regardless of computational time, the split basis set LANL2DZ + 6-31G* vs LANL2DZ ONLY to all atoms, which calculation should offer a better result?
    2- How to include the basis set to the .com input file? Let's take an example below.


    ----- .com input file------------

    %nprocshared=8
    %mem=8GB
    %chk=cisa.chk
    # opt B3LYP/GEN pseudo=read geom=connectivity

    Cisa

    0 1
    Pt -0.98014889 -1.12903224 0.00000000
    O -0.98014889 0.82096776 0.00000000
    H -0.98032420 1.14142234 0.90493581
    O -2.93014889 -1.12903224 0.00000000
    H -3.25060347 -2.03241238 -0.05303937
    H 0.02861950 -3.54569859 0.00868705
    H -1.49205651 -3.54569859 0.86927539
    H -1.47700967 -3.54569910 -0.87796248
    H 1.43651746 -1.50543668 0.93595343
    H 1.43651746 -1.75138926 -0.79395268
    H 1.43651797 -0.13027074 -0.14200076
    N 1.07985111 -1.12903224 0.00000000
    N -0.98014889 -3.18903224 0.00000000

    1 2 1.0 4 1.0 12 1.0 13 1.0
    2 3 1.0
    3
    4 5 1.0
    5
    6 13 1.0
    7 13 1.0
    8 13 1.0
    9 12 1.0
    10 12 1.0
    11 12 1.0
    12
    13
    Ali Shokuhi Rad · Islamic Azad University Tehran Science and Research Branch

    It was helpful, Thank you

  • Ahmed Saeed Hassanien added an answer:
    Please, Can anyone state the values of bond energies for homopolar and heteropolar chemical bond of Cd, S, Se, Ge, As, Cu, In and Ir elements?

    Also I want to know If the CHEMICAL BOND APPROACH TO THE STRUCTURES

    is related only for glasses or it can be applied for crystalline structures, too?

    Please can anyone help me to get a reference contains those values ?

    Ahmed Saeed Hassanien · Benha University

    With the help of my Friend Dr. K. Aly I got the tables of the chemical bond energies and their strengths.and also  join the link  www.webelelments.com 

    Thanks for Dr.Gergo Vassilev. and for all followers

  • Sissi De Beer added an answer:
    Can bond be formed during simulation in Lammps?

    I am working with crosslinking of polymers. during simulation wanted to make bond. is it possible to do in lammps? how to account for the forcefield parameter for the newly formed bonds during simulation. 

    Sissi De Beer · Universiteit Twente

    You can create bonds using fix bond/create: http://lammps.sandia.gov/doc/fix_bond_create.html

    Within this fix, you can define the bond-type (defined with the bond style etc.) of the bond you want to create. 

  • Bartosz Trzaskowski added an answer:
    How to get Fe Atomic Energy using G09?

    I want to calculate the energy of Fe atom. In G09, orbitals occupancies are integer and accordingly one electron occupies one of the down spin d states. This makes the d state non degenerate. So, I would appreciate if somebody kindly inform me the way to calculate the atom energy.

    Bartosz Trzaskowski · University of Warsaw

    The ground state electron configuration for Fe is [Ar],3d6,4s2 . If you provide Gaussian with the proper multipilicty (2S+1 = 5), you should obtain the proper energy for the proper 5D4 term.

  • Saikat Mukherjee added an answer:
    What is the use of Hessian in computational chemistry?

    Couldn't figure out the use of the Hessian matrix in computational chemistry.

    Saikat Mukherjee · Indian Association for the Cultivation of Science

    Yes, I agree with the above answers. Moreover, one can obtain the normal mode coordinates by calculating Hessian matrix followed by the Willson matrix. 

  • John Clare asked a question:
    What might cause persistently inflated (>1.1) values of r-hat in a community occupancy analysis?

    Hi all, I'm trying to fit a couple of community occupancy models and am noticing that r-hat values for certain parameters are well above 1.1 (in the 1.3 - 1.6 range) even with fairly long runs (like, 200,000 iterations w/ 100,000 burn-in).  The model structure includes Bernoulli inclusion parameters associated with all beta parameters.  At any rate, the problematic r-hat values are consistently associated with the precision hyper-parameters for the betas.  Covariates with essentially no model support seem to converge slightly better (or at least have lower r-hats for the precision hyperparameter) than covariates with some support.   Strangely, these r-hat values also seem to stabilize pretty quickly (like, the difference between 15,000 iterations and 50,000 iterations is minimal). I'm curious to hear if anybody else has encountered this.  My kind of desperate explanations are

    1. The model just needs to be run out longer.
    2. I should increase the thinning rate (the trace-plots indicate that the tau chains will occasionally make pretty massive leaps that might be inconsequential if culled by thinning).
    3. This is related to the Bernoulli inclusion parameters turning the betas on and off, and r-hat wouldn't be expected to approach convergent values unless the inclusion probability were very close to 0 or 1.
    4. This is related to tau hyper-parameters themselves, which might not be expected to be distributed roughly normally.
    5.  The taus are derived nodes based upon stochastic sigma hyperparameters, and I should be tracing the latter instead.

    Sorry for the book.  Thanks for any help!

  • How to make up a input file using MRMP calculation in Gamess ?

    I wanted to calculate excited state propeties of molecule considering double excitation. From literature I know how to determine the character of excited state of pentacene,tetracene etc. ,MRMP method has been shown to be accurate for excitation energies .So if anyone knows how to make a input file in gamess ,please help me.

  • Milagros Avendaño added an answer:
    How can we prove the mechanism of DA reactions with Gaussian?

    I have Gaussian output data and I want to prove mechanism of Diels Alder 

    Milagros Avendaño · Central University of Venezuela

    If you have experimental data from your reaction you can run the simulation to find the transition state, compute the theorethical values and see how close the proposed mechanism is from the real one.

  • Anatoly Belonoshko added an answer:
    What will happen if we simulate gases at low temperature?

    I tried simulation of liquid oxygen at 70 K but after NVE simulation temperature is rising to 80-90 K. which is the boiling point of oxygen. I wanted to simulate liquid oxygen. Is it possible to do by MD simulation.

    Anatoly Belonoshko · KTH Royal Institute of Technology

    When you start an MD simulation, your system, as a rule, is not at equilibrium. Therefore, it takes some time to equilibrate it and, during the equilibration period, the temperature can rise. One needs to scale temperature to the desirable one during the equilibration period or control T in some way. In the case of oxygen there is a possibility that the internal (vibrational) degree of freedom will contribute to the rising of T and it might take quite some time to equilibrate translational and vibrational degrees of freedom. Also, please consider that you are dealing not with oxygen but rather with a model of oxygen. And the model of oxygen can have very much diffferent boiling point as compard to the experimental one. It depends on the quality of the model. The determination of the boiling point is a problem in itself.

  • A.s. Martins added an answer:
    How can I build an input file for hetero bilayers in quantum espresso?

    As both the layers have different cell dimensions.

    A.s. Martins · Universidade Federal Fluminense

    Dear Sanjay,

    if you want different cell dimensions for both layers, you have to modify the positions of the B and N atoms. Notice that for the C atoms, the value 0.7075 was taken as half of C-C distance. In this way, you have to put the half of the B-N distance for the B and N atoms. I don't know this distance, but if it is 1.20 Angstrons, the positions would be:

    B   -0.600   0.000   d

    N    0.600   0.000   d

    I hope this can help you. Regards,

    Adriano

  • Mehdi Irani added an answer:
    What is the key word for single point calculations with the CPCM solvation model using Gaussian 03?

    What is the key word for single point calculations with the CPCM solvation model using Gaussian 03?

    Is it necessary to include a radius in the calculations?

    Mehdi Irani · University of Kurdistan

    Thank you everybody for his answer.

  • Iresh Gallindawatte added an answer:
    How can I increase the memory allocation of gamess using the keyword as MWORD?

    when I  suppose to run a .inp file using GAMESS it fails with saying as not enough memory allocation there is solution to use the keyword typing on avogadro but it didn't work ,plz help 

    Iresh Gallindawatte · University of Peradeniya

    increasing the MWORDS capacity up to 200 makes the compilation done ,thank in advance

  • Alan Zhong Li added an answer:
    How can I get a good contact angle value from the droplet-sample surface image?

    I used Attension Theta to measure the water contact angle of my sample. Due to some problems with curve fitting, the contact angle value could not be given by the software. Now I have the image of droplet-sample surface. Is there any software to calculate the contact angle value from the image? Thank you!

    Alan Zhong Li · Nanyang Technological University

    Many thanks to you all, esp. Dipak Giri. LBADSA is very powerful and my problem has been wonderfully solved!

  • Maciej Pyrka added an answer:
    Is it possible to calculate energy of vibrational excited states in GAMESS??

    Now, I just declare the number of states by using NSTATE flag. I supposse this flag concerns electronic states. What about vibrational?? The issue is about absorption, I try to determine wavelength of maximum of absorption

    Maciej Pyrka · University of Warmia and Mazury in Olsztyn

    I'll do that. Thank you for all hints, Eugene.

    Regards

    Maciej

  • Mohammadreza Rezaee added an answer:
    How do you calculate vertical detachment energy for a "Dipole Bound Anion"?

    Calculating vertical detachment energy or electron affinities for a "Dipole Bound Anion" is not as straightforward as the "Valance Bound Anion".  I was wondering if anyone had experience with  "Dipole Bound Anion". It is usually in the order of few Milli-electron volts.

    Thanks!

    Mohammadreza Rezaee · University of Tennessee

    Thank you so much for your kind attention and answers.

  • Yahya Jani added an answer:
    Is solution of population balance equation based on birth and death model?

    I am working with modelling of liquid-liquid extraction and using the birth and death model and the population balance equation. I am wondering if there is any program which have the ability to solve this model?

    Yahya Jani · Linnaeus University

    thanks for everyone

  • Justin Lemkul added an answer:
    How can one calculate free energy of adsorption and aggregation in MD simulations?

    Hi dear all,

    I study adsorption of a single molecule (m) onto a surface (s) in the presence of water (w) using DL POLY code. And also aggregation of two similar molecules in presence of water.

    Well in case of adsorption if we had a vacuum (water did not exist in system), one can easily calculate free energy of adsorption like this:

    E_adsorption=E_(s+m) - E_s - E_m

    Where E_(m+s) is total energy of system after adsorption.

    But my problem is when we have water in system, I suppose we must write:

    E_adsorption=E_(s+m+w) - E_s - E_(m+w)

    And I don't know how to evaluate E_(m+w)? Should I run a single molecule in exact number of water molecules same as total system? What would be my dimensions?

    And also in case of aggregation, what would be the equation for E_adsorption?

    I know that PMF and MSD of adsorbent also can be used for this calculation, but It is not that much easy to calculate them using DL POLY.

    Justin Lemkul · University of Maryland, Baltimore

    Again, that's not a free energy.  That's one of the main problems in obtaining free energies from MD simulations, in general.  There is no entropic term, though the potential can give you insight into enthalpic contributions.  The correct way to do what you want is to obtain a PMF along a suitable (in this case, linear) reaction coordinate.

  • Felipe Schneider added an answer:
    How do I define FRAGOCCUPATIONS in ADF 2013?

    How should one define the FRAGOCCUPATIONS keyword within a ADF 2013 input file? I am using an all-electron basis set.

    Felipe Schneider · Federal University of Santa Catarina

    Thanks Paul!

  • Philip James Hasnip added an answer:
    Is it reasonable my volume versus energy minima is coming at -40kb pressure ?

    I am using VASP code when I am doing pure LaVO4 unit cell structural optimization then volume verses energy minima is coming at 1.4 kb pressure but when I am doing with Eu doping 5*1*1 supercell minima is coming at -40kb. Is it reasonable ?

    Philip James Hasnip · The University of York

    Adding Eu may well change the symmetry of the crystal, did you optimise the lattice before you started your E-V curve calculations? I assume you're using a finite-basis-set correction, but are you sure your plane-wave cut-off is high enough to capture the main stress contributions? The FBSC can only correct energies and stresses which are already reasonable.

    It might be worth trying a 5x2x2 supercell as well to see whether the periodic interaction is significant -- if this is too expensive, you could try shifting your k-point set origin to (0.25,0.25,0.0) and see whether it makes any difference (assuming you're using a gamma-point centred grid to start with). 

    (I'm assuming you've re-converged with respect to plane-wave energy cut-off and k-point sampling when you add Eu, but if not then you should definitely do that first.)

    It is of course possible that you're getting the correct answer, but I would check these things first. Apologies if this is not completely relevant, I use CASTEP and am not familiar with VASP specifically, but they are both plane-wave DFT codes so the principles are the same.

  • Ahmad Bahmani added an answer:
    How to draw a hexagonal crystal in Materials studio (CASTEP)?

    I am going to draw a hexagonal crystal for pure Mg, MgCl2 and solid solution mg phase with Materials studio. But I found some problem in drawing the crystal.

    For example for the case of Mg2Ca, I built a P63/mmc(194) crystal. Then I added Mg atoms in (0, 0, 0) locations. 6 atoms appeared in the screen. Then I added Ca atoms in the (0.33, 0.67, 0.062) but it seems that 8 Ca atoms were added which half were overlapped with the rest (see the picture). 

    I can not understand based on which formula these atoms are added and how can I modify just single atom.

    I extracted the location of atoms from this paper. 

    http://yadda.icm.edu.pl/yadda/element/bwmeta1.element.elsevier-5e87325f-c99e-30af-a496-17eb5db795dc

    Kindest Regards

    Ahmad Bahmani · Seoul National University

    Thank you so much for your comments.

  • Sayed Muktar Hossain added an answer:
    How to obtain QST2 Calculation to find the transition state?
    I have a problem doing the qst2 calculation. My purpose is to find the transition state of the decomposition mechanism process. I have already used the scan process to find the maximum energy of the molecule and use the opt=(ts,noeigen) to optimize the transition state. But I can't find any imaginary frequency. Then I tried use qst2 calculation to find the transition state. The results from qst2 are error in internal coordinate system and error termination via Lnk1e in/pkg/chem/gaussian/g09c01/g09/l103.exe. Is there any ways to find out the transition state or some suggestion to do this calculation?
    Sayed Muktar Hossain · Indian Institute of Technology Bhubaneswar

    Mohamed Aboelnga sir,

    That problem has solved. Can u help me plz to optimize excited structure in solvent medium.

  • Miguel Mompeán added an answer:
    How do I determine whether a bond is present using NBO from Gaussian09?

    I’ve been asked to study using DFT (wb97xd/lanl2dz). Prior to introducing Cu(2+), my structure seems reasonable enough yet when Cu(2+) is introduced at a particular site, the C-C bond prior to the carboxylate (we knocked off the hydrogen from the COOH group due to its absence from our mass spec data) group yields a distance of 1.88 angstrom. The structures have been tightly optimised, and I have tried this out on a different control with the same result.

    My question is how do I go about understanding whether there is a bond, or no bond at all using NBO. I have looked at my NBO output and found the BD and BD* entries:

    1. (0.97584) BD ( 1) C 1 – C 2
    ( 47.03%) 0.6858* C 1 s( 25.63%)p 2.90( 74.37%)
    0.0001 -0.4963 0.0999 0.5583 0.0288
    0.6491 0.0140 0.0981 0.0049
    ( 52.97%) 0.7278* C 2 s( 11.14%)p 7.98( 88.86%)
    -0.0001 -0.3314 0.0399 -0.6464 -0.0426
    -0.6385 -0.0367 -0.2441 -0.0184

    I am not a pure chemist to any degree, but I assume the C-C occupancy of 0.97584 implies that no bond is formed? i.e., a single electron on the bonding valence suborbital. However, when I investigate further, it appears as though no occupancies for BD appear to be above 1, which seems odd as I would have expected a lot of values about 1.9. Below are a few more NBOs straight out of the log file:

    (Occupancy) Bond orbital/ Coefficients/ Hybrids
    ---------------------------------------------------------------------------------
    1. (0.97584) BD ( 1) C 1 - C 2
    ( 47.03%) 0.6858* C 1 s( 25.63%)p 2.90( 74.37%)
    0.0001 -0.4963 0.0999 0.5583 0.0288
    0.6491 0.0140 0.0981 0.0049
    ( 52.97%) 0.7278* C 2 s( 11.14%)p 7.98( 88.86%)
    -0.0001 -0.3314 0.0399 -0.6464 -0.0426
    -0.6385 -0.0367 -0.2441 -0.0184
    2. (0.99644) BD ( 1) C 1 - O 13
    ( 31.38%) 0.5602* C 1 s( 37.17%)p 1.69( 62.83%)
    0.0001 0.6079 0.0465 -0.2135 -0.0086
    0.6909 -0.0369 -0.3219 0.0202
    ( 68.62%) 0.8284* O 13 s( 37.72%)p 1.65( 62.28%)
    0.0000 0.6136 0.0266 0.3119 -0.0100
    -0.5957 0.0211 0.4122 -0.0156
    3. (0.99695) BD ( 1) C 1 - O 14
    ( 29.66%) 0.5446* C 1 s( 14.77%)p 5.77( 85.23%)
    0.0000 0.3830 0.0321 0.0542 -0.0281
    0.1042 0.0036 0.9151 -0.0150
    ( 70.34%) 0.8387* O 14 s( 14.01%)p 6.14( 85.99%)
    0.0000 0.3737 0.0205 -0.7304 0.0181
    0.3934 -0.0082 0.4138 0.0086
    4. (0.99576) BD ( 2) C 1 - O 14
    ( 30.93%) 0.5561* C 1 s( 23.68%)p 3.22( 76.32%)
    -0.0002 0.4838 0.0527 0.7945 -0.0296
    -0.2866 -0.0135 -0.2199 -0.0185
    ( 69.07%) 0.8311* O 14 s( 22.60%)p 3.42( 77.40%)
    0.0000 0.4747 0.0261 -0.2006 0.0201
    0.0712 -0.0080 -0.8532 0.0161

    Many thanks

    Anthony

    Miguel Mompeán · Spanish National Research Council

    Hi Anthony, 

    I agree with Martin, you are dealing with an open-shell system and that is why you see those occupancy numbers. Regarding your first question in the former post, your output indeed tells that there is  a C1-C2 bond, and you can see what the overlap between the hybrids is (sp^2.90 & sp^7.98, respectively).

    As Martin pointed, you should look for both the alpha and beta spin orbitals. You can achieve this by searching for these two entries in your output file:

    "NATURAL BOND ORBITAL ANALYSIS, alpha spin orbitals"

    "NATURAL BOND ORBITAL ANALYSIS, beta spin orbitals"

    (In the case of closed-shell systems you only have " NATURAL BOND ORBITAL ANALYSIS")

    Cheers,

    Miguel

  • Abolfazl Noorjahan added an answer:
    Can anyone provide information about optimum specification requirements for the computer to do molecular dynamics simulation for 2000 atoms?

    We are working on graphene nanofillers and planning to do simulation using molecular dynamics, for this we need an optimum specification requirements for the computer (RAM, processor, speed, and some basic information) to do molecular dynamics simulations for 2000 atoms. It will be helpful for us if somebody provides an information regarding the same.

    Abolfazl Noorjahan · University of Alberta

    It depends on the software you  are planning to use. If it support GPU (CPU and RAM are not problem anymore) so even with a moderate graphic card (CUDA capable) you can handle your case. But if you don't have access to GPU enabled code, Just go for more number of cores rather than higher clocks, parallel MD codes can benefits from different cores to accelerate the calculations (dedicated cores to PME and neighbor searching and etc.). For this number of atoms the RAM does not concern you at all. 

  • Filippo Lipparini added an answer:
    Can anybody help me? I am getting the following error in gaussian 03"no lower point found --run abroted via linkle termination /508"?

    Hi I am optimizing the 15 atoms file with the following path

    %mem=62MB
    # opt=(cal call,max cycle=512) pbepbe/6-311++g(d,p) s cf=(QC,max cycle=2048)

    I am getting this error

    Search did not lower the energy significantly.
    Scaled steepest descent with Shift=0.075 failed.
    Search did not lower the energy significantly.
    No lower point found -- switch to steepest descent.
    Search did not lower the energy significantly.
    No lower point found -- run aborted.
    Error termination via Lnk1e in C:\G03W\l508.

    I tried my ways like using keywords QC,increasing cycles,ultra fine etc. I am not getting but if I optimized the same file with b3ylp/6-311++g(d,P), I got results but I want to know how to solve. Can anybody help me?

    Filippo Lipparini · Johannes Gutenberg-Universität Mainz

    Molecules containing transition metals are always a pain...

    I think that the main problem here is to get the SCF to converge: the geometry optimization shouldn't be an issue.

    I would recommend to try with Fermi broadening - SCF(Fermi) - using Int(Grid=Ultrafine).

    If this doesn't work alone, I would combine it with the quadratically convergent SCF:

    SCF(Fermi,XQC,MaxConventionalCycles=30)

    always using the Ultrafine grid.


    Good luck!

  • Anthony Nash added an answer:
    Can I implement covalent bonds in Gromacs in the absence of dihedral and/or angle parameters?

    I have two zinc coordinations in my globular protein, using Amberssff in Gromacs. Partial charges have been calculated for both using PyRED. One zinc remains in place using a non-bonded model, mainly due to the fact that it is buried in the protein and the only electronegative neighbouring atoms are the coordinating nitrogens on its four histidines. 

    The second zinc complex uses water as a fourth donor. Thus I am trying to use covalent bonds to keep the zinc in place with its three histidines. I have partial charges for the histidines, however, when I have tried to refit the unknown force field parameters for the Zn-N bonds using PyRED I get nothing because they don't exist in the Amber bonded parameter data set. It turns out I need to supply a frcmod.user file to make up for everything missing in the frcmod.unknown (all my Zinc related parameters). Pretty understandable. 

    I was able to find Amber Zn-N bond distance force constants and bond distance equilibrium values, and even so for N-Zn-N angles. Unfortunately the dihedral angles have been a little trickier to find. My first questions involves the nature and number of dihedral angles. With zinc surrounded by three histidines (plus one water), donating nitrogen to the first coordination sphere, what particular dihedral angles should I include in an MD forcefield? 

    Zn - N - C - C

    Zn - N - C - N

    N - Zn - N - C (db bonds to other carbon on ring)

    N - Zn - N - C (sg bonds to the second nitrogen on the ring)

    My second question. Is it possible to run Gromacs and does it make sense to implement only [ bonds ] entries for Zn-N* entries? Or do I need to also have angles and dihedrals?

    Thanks

    Anthony

    Anthony Nash · University College London

    Thanks Justin, that was of huge help. I now have a fully parameterised force field. Fingers crossed that I get it through grompp and an energy min stage! 

  • Justin Lemkul added an answer:
    Where can I find OPLS AA dihedral angles for 1,4 polybutadiene?

    Good day

    I wish to simulate 1,4 polybutadiene but when I run the energy minimization after solvating the box with polymer inside, I get an error that basically tells me that a dihedral angle is not defined. I am looking for the CM CT CT CM (=C-C-C-C=) dihedral to use in gromacs/OPLS AA force field. In the force field only the CM CT CT CT (=C-C-C-C-) dihedral is available. Does anybody know how I could get this information?

    Thank you for your time

    Justin Lemkul · University of Maryland, Baltimore

    ATB is for Gromos force fields; the parameters it gives will not be compatible with OPLS-AA.

    It is rather straightforward to derive parameters for OPLS-AA with QM dihedral scans. That is the best option when information for a given interaction is missing.

  • Grant Hill added an answer:
    Can you recommend a good overview of halogen bonding?

    Thanks. 

    Grant Hill · The University of Sheffield

    You might also find this perspective interesting, it is focused on experimental results of small gas-phase complexes, but I find it helps with understanding the fundamentals. 

  • Shuangyan Zhou added an answer:
    How do I scale epsilon parameters of Lennard-Jones term in .top file?

    Hi all,
    I am trying to run REST in GROMACS following the way proposed by tsuyoshi terakawa. In their method,they implemented REST by rescaling the force-field parameters without even changing the code. I have also searched in the mailing list and found that we can manipulate the scale parameter in ffnonbonded.itp and ffbonded.itp as well as the .rtp file for charges to construct the .top of highest "temperature" which corresponds to lambda=1.Taking the two states (the lowest "temperature" corresponds to lambda=0 regard as state A and highest temperature corresponds to lambda=1 regard as state B) into the same .top file, and then we can directly use the Hamiltonian REM routine of GROMACS 4,which is based on the λ-dynamics and the linear combination potential scheme of the two-ends potentials(I do not know whether my understanding is right?).
    I add the parameters of state B in to the topology A following the 5.7.4 "Topologies for free energy calculations" in GROMACS manual.The bond scaling parameters can be added in [bonds] with dA kA dB,kB,where the dA, kA, stand for the bond parameters of state A, and the dB, kB stand for the parameters of state B.Other scaling parameters such as [angles],[dihedrals] can be treated as the same way. My question is how to add the epsilon parameters of Lennard-Jones of state B into the .top file? The force field that I used is OPLS-AA force field,is it true to add the epsilon value in the [pairs] part? I do not know in [pairs] with the format of :ai aj funct c0 c1 c2 c3,what c0,c1,c2 and c3 stands for?
    Would you some body give me some suggestions? thanks very much

    Shuangyan Zhou · Lanzhou University

    Hi Jamoliddin,

    Thanks for you kind help ,that helps me a lot

  • Zahra Mousavi added an answer:
    I want to simulate a system containing protein and heavy metal, is it possible to do it with GROMACS? Which force field is appropriate?

    This is with regards to adsorption of heavy metals on proteins.

    Zahra Mousavi · Tarbiat Modares University

    thank you for your help...

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