[gmx-users] Check for bad contacts and/or reduce the timestep
schlesi at uni-mainz.de
Tue Dec 15 15:07:46 CET 2009
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.
> 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
> 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:
>> 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 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
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