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" <[email protected]>
Subject: Re: [gmx-users] Check for bad contacts and/or reduce the
timestep
To: "Gromacs Users' List" <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
[email protected] 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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