[gmx-users] Check for bad contacts and/or reduce the timestep

[nishap.patel at utoronto.ca]

Hi, I tried energy minimization and I am getting the error while I am  
running the minimization step. But then I still tried to carry on with  
normal md-simulation, and it was fine, but I am sure it won't give me  
the result that it should. Is there a reason for that? I have tried  
very low energy steps as well, but I am still getting the error.
-Nisha




Quoting Thomas Schlesier <schlesi at uni-mainz.de>:

> You can try a normal md-simulation after the energy minimisation, with
> a very low timestep (around two orders of magnitude lower, for 5ps).
> For this use no T-couple, or if with, then with a very low temperature.
> I had a case where i had a box of well ordered benzene molecules and
> only energyminimization didn't helpt much (In normal md simulation i
> got many lincs warning form the beginning). After the short
> NVE-md-simulation the benzene molecules weren't ordered and after a
> second energy minimization it was possible to do a normal md simulation
> at 300 K without any lincs warnings.
> Could be possible that the same protocol works also in your case, else
> follow Justin's advice.
> Greetings Thomas
>
>> Message: 3
>> Date: Mon, 14 Dec 2009 14:09:47 -0500
>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] Check for bad contacts and/or reduce the
>>        timestep
>> To: "Gromacs Users' List" <gmx-users at gromacs.org>
>> Message-ID: <4B268D7B.1060500 at vt.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>>
>> nishap.patel at utoronto.ca wrote:
>>
>> <snip>
>>
>>
>>> Steepest Descents converged to machine precision in 34 steps,
>>> but did not reach the requested Fmax < 10.
>>> Potential Energy  = -3.7206969e+04
>>> Maximum force     =  2.0111207e+04 on atom 1217
>>> Norm of force     =  6.9283209e+02
>>>
>>> I don't understand constraints I need to turn off, since I haven't
>>> mentioned any in my grompp file.
>>>
>>>
>>
>> This is just generic advice that mdrun provides.  The fact is your starting
>> structure contains atomic overlap or clashes that cannot be   
>> resolved by energy
>> minimization.  Have a look at the trajectory and see if you can get  
>>  some insight
>> into where things are going wrong (since problematic atom numbers are being
>> printed, and perhaps re-consider how you built your system.
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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