Flávio Freitas

Centro de Biotechnologia de Amazônia | ABC · Department of Chemistry

I am working with large amounts of pulp (in blocks, like reams of paper) and need to solubilize it without grinding.

I tried some organic solvents and solvent mixtures for solubilization, but I could only see the swelling of some surface sheets of cellulose (which is a good thing, but the full swelling of the sheet would be better).

I thought of using large amounts of acid, but it could make my project unfeasible.

Would you have any ideas?

Thank you in advance if you can help me.

Dears, 

I am a beginner in molecular dynamics and I need your help to solve this problem.

I am running a simulation using water/surfactant/oil/surfactant/water with 28438  atoms at 323K and 98 atm, 3ns NPT to shrink the box (5x5x12 nm3), obtaining the right density and 2 ns NVT.  

At NPT, the pressure is very good, near 100 atm without big fluctuations. But at NVT the pressure goes down, remaining in equilibrium in 50 atm. 

My question is: how should I change the script to maintain the pressure close to 98 atm during NVT steps?

I tried do solve this problem reading the LAMMPS Manual and also here the Mailing Lists. But I was not able. 

My Script:

pair_modify   mix arithmetic tail yes kspace_style  pppm 1.0e-4 minimize      1.0e-4 1.0e-6 100 1000 reset_timestep 0 fix           SHAKE all shake 0.0001 20 0 b 1 3 9 11 a 1 neighbor      2.0 bin timestep      1.0 variable      TK equal 323.15 variable      PBAR equal 98.6923 velocity      all create ${TK} 123456 rot yes mom yes dist gaussian variable      nsteps equal 2000000                 # 2000                    #  variable      nptsteps equal 3000000                 # 2000                    #                                                                               variable      nhalf equal ${nsteps}/2 variable      nprint equal ${nsteps}/2000 variable      ndump equal ${nsteps}/100 variable      xyzdump equal ${nsteps}/20 variable      padval equal 7                       # 5 variable      nrdf equal 100                       # 10                       #  variable      Tdamp equal 100                      # 10                       #  variable      Pdamp equal 500                      # 50                       #  # fix         1 all nvt temp ${TK} ${TK} ${Tdamp} fix           1 all npt temp ${TK} ${TK} ${Tdamp} iso ${PBAR} ${PBAR} ${Pdamp} variable      xPress equal c_thermo_press[1] variable      yPress equal c_thermo_press[2] variable      zPress equal c_thermo_press[3] variable      IFT equal (0.5*lz*(v_zPress-0.5*(v_xPress+v_yPress))*0.0101325) dump          2 all image ${xyzdump} nvt.*.jpg type type zoom 1.0 adiam 1.5 size 720 1280 dump_modify   2 pad ${padval} thermo_style  custom step pe ke etotal temp press density vol lx ly lz pxx &               pyy pzz  pxy  pxz  pyz  v_IFT thermo        ${nprint} run           ${nptsteps} unfix         1 fix           2 all nvt temp ${TK} ${TK} ${Tdamp} # fix         2 all npt temp ${TK} ${TK} ${Tdamp} iso ${PBAR} ${PBAR} ${Pdamp} run           ${nsteps} write_restart restart.*.lmp write_data    nvt.*.data

Thank you so much for your attention. 

Kind regards, 

Dears,

I am a beginner in simulations.

I am trying to put some surfactants in a water/oil interface, fixing * and orienting the molecules at the interface with the hydrophilic head directed towards the water and the hydrophobic towards the oil.

Using Packmol I was able to create the box with water/surfactant / oil/surfactant/water, but I could not create a space between the water and the oil to place the surfactants and I could not even fix the molecules.

* I need to fix them so they do not interact with each other at the beginning of the simulation.

** I need this empty space to vary the number of molecules in the interface and then decrease the size of the box using NPT.

In the Packmol user guide, I saw in the examples that you have how to fix only one molecule:

"structure molecule.pdb

number 1

center

fixed 0. 0. 0. 0. 0. 0.

end structure "

In this example, one molecule will be fixed with its center the origin and no rotation, but I do not know if I would have to fix several molecules at the same time.

I really appreciate it if you may help me.

Kind regards.

Hello,

I am beginner in Materials studio software and also in Molecular dynamics and I am needing to build a silica nanosphere with different numbers of hydroxyl groups to adsorb some molecules. Could someone help me to solve this issue?

Thank you.