[gmx-users] mdrun creates pdb files!

Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl
Wed Feb 4 10:14:00 CET 2004

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. 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.



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
>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!!

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