[gmx-users] Fwd: How can i run my system successfully?
jalemkul at vt.edu
Sun Dec 8 23:08:47 CET 2013
On 12/8/13 2:38 PM, bahareh khanoom wrote:
> Dear friend
> very thanks for your answers
> There is one important thing that i must say, after minimization energy i
> run my system for nvt equilibration in " 500 ps " and run done without any
> problem ,
> then i applied the output file as input file for nvt equilibration in "15
> ns" , but during first "1 ns" run exit:
> 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 your suggestion for solving this problem?
The same as I suggested in my previous message. You need to (scientifically!)
diagnose the possible sources of error.
> thanks in advance
> On Sat, Dec 7, 2013 at 4:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 12/7/13 4:51 AM, bahareh khanoom wrote:
>>> 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.
>> How do these charges compare with existing charges for similar functional
>> groups in the force field? AFAIK, there is no hard evidence as to which QM
>> method will give the best results from Gromos96 force fields.
>> so ,what is the reason?
>> It is hard to say at this point, but one solution is to simulate each
>> component individually to verify that their topologies are correct and that
>> your .mdp settings are appropriate (though they look reasonable on first
>> See also http://www.gromacs.org/Documentation/Terminology/
>> 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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Justin A. Lemkul, Ph.D.
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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