[gmx-users] Fwd: How can i run my system successfully?
bahareh.ghasemipoor at gmail.com
Sat Dec 7 10:52:00 CET 2013
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
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
>> 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 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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