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

[Thomas Schlesier]

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
>
> ========================================