[gmx-users] mdrun creates pdb files!

[Stud_Psychopharm]

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." - 
R.Buckminster Fuller 

Blaise M.
Graduate Student,
Department of Psychopharmacology,
National Institute of Mental Health And Neuro Sciences (NIMHANS),
Bangalore-560029,
India. Tel: 91 80 6995112.


-----Original Message-----
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 
> clearer.
> 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.
> The 
> potential energy should be negative for a solvated system. It looks
> like 
> 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
> objects?
> 
> 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.
> 
> Greetings,
> 
> Tsjerk
> 
> 
> Madhuri Agashe wrote:
> 
> >Yes, that does help.
> >
> >But I cannot figure out what the problem might be. Here are some more
> inputs
> >on my system: 
> >It consists of an methyl terminated SAM surface with a protein
> fragment
> >adsorbing to it. The main aim of the simulation is to study the
> adsorption
> >behavior.
> >After solvating the system, I ran the genion command to replace some
> solvent
> >atoms by charged NA/CL ions.
> >Then an mdrun was run for energy minimization. Now this did say at the
> end
> >of the run that the system did not converge in 40 steps. Could that be
> the
> >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
> configuration?
> >
> >I really appreciate your help!!
> >Thanks,
> >madhuri
> >
> >
> 
> 
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