[gmx-users] continuation, gmx-users Digest, Vol 102, Issue 99

[Justin Lemkul]

On 10/16/12 1:14 PM, Ali Alizadeh wrote:
> Dear Justin
>
> In your opinion, Why did not i get a symmetric results of number density?
>

The .mdp file does not give any really useful information for this problem, 
except to show that you're using NPT, which I suspect might contribute to the 
problem.  Without plots and hard numbers, it's all hand-waving at this point.

-Justin

> this is my md.mdp file:
>
> title		= OPLS
> define		= 	;
> ; Run parameters
> integrator	= md		;
> nsteps		= 1000000		;
> dt		= 0.001		;
> emtol		= 10.0
> emstep          = 0.00001
> ; Output control
> nstxout		= 10		;
> nstvout		= 10		;
> nstenergy	= 10		;
> nstlog		= 10		;
> nstxtcout       = 10
> xtc_precision   = 10
> ; Bond parameters
> continuation	= no		;
> constraint_algorithm = lincs	;
> constraints	= all-bonds	;
> lincs_iter	= 1		;
> lincs_order	= 4		;
> ; Neighborsearching
> ns_type		= grid		;
> nstlist		= 1		;
> rlist		= 1.0		;
> rcoulomb	= 1.0		;
> rvdw		= 1.0		;
> ; Electrostatics
> coulombtype	= PME		;
> pme_order	= 4		;
> fourierspacing	= 0.16		;
> ewald_geometry  = 3d
> ; Temperature coupling is on
> tcoupl		= berendsen	;
> tc-grps		= System	;
> tau_t		= 0.1	;
> ref_t		= 240	;
> ; Pressure coupling is on
> pcoupl		= berendsen	;
> pcoupltype	= isotropic	;
> tau_p		= 2.0		;
> ref_p		= 300.0		;
> compressibility = 4.5e-5	;
> refcoord_scaling = com
> ; Periodic boundary conditions
> pbc		= xyz		; 3-D PBC
> ; Dispersion correction
> DispCorr	= EnerPres	;
> ; Velocity generation
> gen_vel		= no		;
>
>
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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