[gmx-users] bad contacts on lipid tails

[Justin Lemkul]

On 6/14/17 5:18 PM, Mohsen Ramezanpour wrote:
> Hi Justin,
> 
> Thanks for your reply,
> 
> Here are the outputs for EM step:
> 
> Steepest Descents converged to Fmax < 100 in 5198 steps
> Potential Energy  = -2.6418572e+05
> Maximum force     =  9.5666359e+01 on atom 54770
> Norm of force     =  5.7127428e+00
> 
> It seems okay to me.
> 
> I chose the setting you mentioned.
> 
> Interestingly, it also works for MD with dt=1 fs. Not for dt=2 fs, though.
> Based on visualization, some lipid chains are crossed which I think this
> cause the problem. Not sure how can I fix them.
> 

Surprising.  With such a low force, I wouldn't expect there to be any overlap or 
detrimental close contact.  An initial equilibration with dt = 1 fs is a 
possibility, or a more robust method for constructing the system, whatever that 
may be.

-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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