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

[Justin Lemkul]

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.

-Justin

> thanks in advance
> bahar
>
>
> 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
>> glance).
>>
>> See also http://www.gromacs.org/Documentation/Terminology/
>> Blowing_Up#Diagnosing_an_Unstable_System.
>>
>>
>> -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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-- 
==================================================

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

==================================================