Re: Error in membrane protein simulation

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Sep 03 2012 - 15:51:35 CDT

After you run your minimization, write a new PDB file and then continue the equilibration with that as the reference for the harmonic restraints.

On Sep 1, 2012, at 1:59 AM, amin_at_imtech.res.in wrote:

> Dear all,
> I am trying to simulate a protein embedded in a POPC membrane. I am
> following the NAMD tutorial on membrane proteins. When I go to the first
> equilibration step using constraints mentioned in the step "melting of
> membrane" I get "Constraints failure in rattle algorithm" with rigidbonds
> all and "Atoms moving too fast" with rigidbonds water. I looked for the
> solutions in mailing list and tried 1) decreasing time step to 0.5, 2)
> increasing minimization steps from 1000 to 10000, 3) increasing
> pairlistdist to 16, 4) setting margin upto 10, 5) gradually heating at a
> slow rate. Also I noticed that during minimization I have energies
> 9999999. I have checked the atoms mentioned in the error file visually
> and they are distributed throughout the membrane.There are more than 5000
> of them. I made the membrane using VMD membrane plugin. Can someone
> please tell me where I might be making an error.
>
> Regards.
>
> Amin.
>
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