[gmx-users] temperature problem

[Justin Lemkul]

On 6/5/15 8:09 AM, Lovika Moudgil wrote:
> Hi Justin... Yes I agree my system is behaving absurdly . But I am
> wondering why !!I have done minimization without any error ..here is the
> result ...
> Steepest Descents converged to Fmax < 1000 in 1004 steps
> Potential Energy  = -9.6667906e+05
> Maximum force     =  9.7920349e+02 on atom 796
> Norm of force     =  1.7943926e+01
> ... I have One gold slab ...with golp parameters ..and amino acid on it
> ...in box with water and Na , Cl ions ....Freezing is for gold  only....

So simplify the system - remove the gold layer and see if the remainder works, 
do a system of water + gold, etc.  Your system is more complex than you're 
likely giving it credit for.  Break it down - be scientific!

> System is not that big . And thing is temperature remain at the value (that
> is 300K)  for few time after some time it start behaving weird . If system
> is wrong why its working even for one step ??
>

Probably because the starting configuration is fine, but the trajectory evolves 
in such a way that it produces unreasonable physics.  Freezing is a pretty 
severe perturbation.  Investigate the validity of the force field.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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