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

[David van der Spoel]

Andrea Robben wrote:
> 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

turn off comm_mode = angular
otherwise mdp file looks fine. You could rvdw = 1.4 but otherwise any 
deviations are due to the force field.



>  
> Thanks
> Andrea
>  
> 
> 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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