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

[bahareh khanoom]

Dear friend
thanks for your answer

first i generate" DRG.itp" for adsorbed molecules, by PRODRG server.
next i optimize adsorbed moleculs by gaussian
b3lyp/6-311++g(d) opt Pop=ChelpG
and the end ,i replaced the charges in" DRG.itp" with  charges that
produced by gaussian.

so ,what is the reason?


thanks in advance
bahar







On Fri, Dec 6, 2013 at 7:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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