[gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg

[Justin Lemkul]

On 2/9/15 11:00 AM, Agnivo Gosai wrote:
> Hi Antara
>
> Did you check the plot of the potential energy against the simulation time
> ? You can visualize the convergence of your energy minimisation from the
> above plot.
>

Energy minimization, by definition, converges to some value (but there is no 
time in EM, it's not a dynamical process).  That converged result is what is 
printed.  There's usually nothing informative when EM converges without complaint.

-Justin

> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
>
> On 2/9/15 7:41 AM, Antara mazumdar wrote:
>
>> i got the following result after EM of this system of mine.
>>
>> writing lowest energy coordinates.
>>
>> Steepest Descents converged to Fmax < 1000 in 15280 steps
>> Potential Energy  = -5.0853170e+06
>> Maximum force     =  9.9438867e+02 on atom 179440
>> Norm of force     =  7.8095098e+00
>>    Should i go ahead with NVT and NPT? --
>>
>>
> Is there a reason you think you shouldn't?  What outcome do you expect?
> Does this outcome meet that expectation?  Does the structure look sensible?
>
> -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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