[gmx-users] Fwd: How can i run my system successfully?

[Justin Lemkul]

On 12/6/13 6:06 AM, bahareh khanoom wrote:
> Hi friends
> I want to simulate a system that consists of 2 molecule on the graphite
> surface. To generate " DRG.itp" for adsorbed molecule, I used PRODRG
> server. I applied ffG43a1 for simulation this system. I did minimaization
> energy without any problem, but when i run my system for nvt equilibration,
> run exit. for example:
>
> Step 79777, time 159.554 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.346309, max 1.958716 (between atoms 13 and 15)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>       13     15   90.0    0.1000   0.2959      0.1000
> Wrote pdb files with previous and current coordinates
>
> so, what is the reason?
>

Have you corrected the PRODRG topology?  The charges and charge groups it 
produces are usually very bad, so the simulations are unstable because the 
topology is unsuitable.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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