DMSO dymamic

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1

Hi,

I’m trying to run a nvt (298K) simulation of DMSO

correctly my box simulation has got 68 molecules in a volume of 8000 A.

I fixed molecule during the simulation

Atom Groupings

group DMSO id <> 1 680

END Atom Groupings

fix DMSONVE DMSO rigid/nve/small molecule langevin 298.0 298.0 10. 123
timestep 2
run 2000
unfix DMSONVE
reset_timestep 0

compute T all temp
fix TempAve all ave/time {Ne} {Nr} ${Nf} c_T

variable Dens equal v_nMolecules*{DMSOMoleculeMass}/(vol*{A3_in_mL}) # dens g/mL
fix DensAve all ave/time {Ne} {Nr} ${Nf} v_Dens file DMSO.dens

#give an initial random velocity (corresponding to a temperature equal to 298K)
velocity DMSO create 298 1233 rot yes mom yes dist uniform

#apply Langevin thermostat on water molecules
fix DMSOlang DMSO langevin 298.0 298.0 10. 123

run dynamic at 298K

fix 1 DMSO rigid/nvt/small molecule temp 298.0 298.0 1.0

the results is that the system is not stable and the pressure bad!!

Step Volume Temp f_TempAve Press TotEng PotEng KinEng E_vdwl E_coul E_bond E_angle E_dihed E_impro f_DensAve
0 8000 316.35626 0 56949.474 -2546.5963 -2673.901 127.30472 -409.10877 -1956.5929 256.64339 129.51615 129.15689 0 0
5 8000 -nan -nan -nan -nan -nan -nan -3.9170328 0 -nan -nan -nan 0 1.102758

How I could fix it!

regards

M

2

Your dynamics are bad. Print thermo info every step and see
what goes wrong first.

Steve

3

Hi steve,

In my input there is a group of molecules of DMSO.

Atom Groupings

group DMSO id <> 1 680

END Atom Groupings

in output the code correctly, I think, the code finds

680 atoms in group DMSO
68 rigid bodies with 680 atoms

and I think that I could exclude intertions between atoms of some molecule with neigh_modify command with option exclude

regards

4

I just noticed you are applying 2 thermostats to your rigid atoms,
fix rigid//nvt/small and fix langevin. Not a good idea.

Steve

5

Hi,

I’m testing a small example defining 10 molecules of DMSO
I heve 10 groups, one for every molecule.

With rigid/nvt group 10 and ten groupID, the simulation is ok!
But I’m not increase the number of group > 32 as reported in manual.
How I could fix it?

Al

6

ok, now you are asking something different. The first
Q was about bad dynamics, which I think was due
to using 2 thermostats. You should not do that.

The 2nd Q is about how to use fix rigid. You don’t need
one group per molecule. Either fix rigid or fix rigid/small
will define one rigid body per molecule if you use the
right options. And you only need one group, no
matter how many molecules.

Steve