[gmx-users] mdrun creates pdb files!
stu_psyc at nimhans.kar.nic.in
Wed Feb 4 17:05:01 CET 2004
hope simulated annealing also may helpful to overcome the energy barriers
in this situation.!
"The more we learn the more we realize how little we know." -
Department of Psychopharmacology,
National Institute of Mental Health And Neuro Sciences (NIMHANS),
India. Tel: 91 80 6995112.
From: Tsjerk Wassenaar <t.a.wassenaar at chem.rug.nl>
To: gmx-users at gromacs.org
Date: Wed, 04 Feb 2004 02:25:27 +0100
Subject: Re: [gmx-users] mdrun creates pdb files!
> Hi Madhuri,
> Also having read your mail on the minimization, things are just a bit
> Your system has a potential energy which is way too high (6.9e+10!). No
> wonder your system is exploding as soon as you start the simulation.
> potential energy should be negative for a solvated system. It looks
> you've got some serious overlaps in your initial configuration, which
> the minimizer can't get rid of.
> In setting up the system, have you run simulations of the SAM surface
> and the protein seperately, and are these simulations stable?
> Have you manually positioned the protein at the surface and by chance
> put it too close? And did you change the box dimensions to fit both
> Have you performed energy minimization on the SAM surface with the
> protein in vacuum?
> Either checking/performing these steps can fix the error or can give
> more insight on where things are failing.
> Madhuri Agashe wrote:
> >Yes, that does help.
> >But I cannot figure out what the problem might be. Here are some more
> >on my system:
> >It consists of an methyl terminated SAM surface with a protein
> >adsorbing to it. The main aim of the simulation is to study the
> >After solvating the system, I ran the genion command to replace some
> >atoms by charged NA/CL ions.
> >Then an mdrun was run for energy minimization. Now this did say at the
> >of the run that the system did not converge in 40 steps. Could that be
> >problem with the mdrun failure later?
> >The generation of pdb files occurred immediately after starting the
> >simulation. How can I check for the correctness of the input
> >I really appreciate your help!!
> -- :)
> -- :) Tsjerk A. Wassenaar, M.Sc.
> -- :) Molecular Dynamics Group
> -- :) Dept. of Biophysical Chemistry
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