[gmx-users] Too much movement in molecular crystal simulation

Andrea Robben alrobben at engineering.ucsb.edu
Fri Feb 10 05:12:20 CET 2006

I am trying to simulate stearic acid in a crystal form. My simulation box is a multiple of the unitcell of the crystal and I have 6 copies of the unitcell in each direction.  After I run a NPT simulation at a temperature (300K) the crystal is stable (below the melting temperature) but I have more movement in the individual stearic acids then I would expect.  While they are remaining ordered, the acid group and portions of the alkane tail are rotating so that there is a lot of variability between stearic acids.  This rotating is so much I'm seeing a small shift in the layer spacing in one direction. I am using all-bonds constraints using LINCS and comm_mode = angular.  From the manual it appeared to me that there were corrections to the energy so that the lack of bond vibration is accounted for in the temperature but I wasn't completely sure.  Could the all-bonds LINCS constraint cause more energy to be in bond rotations, would problems with my box (not big enough, etc.) be more likely, or could it be something else?

Below is my .mdp file


title = Stearic acid polymorph C 

cpp = /lib/cpp

include = -I../top

integrator = md

comm-grps = Str 

nstcomm = 1

comm-mode = angular

dt = 0.002

nsteps = 500000

nstxout = 500000

nstvout = 500000

nstlog = 1000

nstenergy = 1000

nstxtcout = 1000

xtc_grps = Str 

energygrps = Str 

nstlist = 5

ns_type = grid

pbc = xyz

;PME protocol: Check it!

;coulombtype = Reaction-field

;rlist = 0.9 

;rcoulomb = 1.4

;rvdw = 1.0

;epsilon_r = 2

coulombtype = PME

rlist = 0.9 

rcoulomb = 0.9

rvdw = 0.9

fourierspacing = 0.12 

pme_order = 4 

ewald_rtol = 1e-5

optimize_fft = yes

;T- and P-coupling: Even if I use PME, just to be safe

tcoupl = Berendsen 

tc-grps = System

tau_t = 0.1 

ref_t = 300 

Pcoupl = Berendsen

pcoupltype = isotropic

tau_p = 1.0

compressibility = 5e-5

ref_p = 1.0

gen_vel = yes

gen_temp = 300

gen_seed = 503114 

constraints = all-bonds
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