AW: Error in membrane protein simulation

From: Norman Geist (
Date: Mon Sep 03 2012 - 01:52:45 CDT


as you did unfortunately not mention which of the energies are 9999999, I can only guess.

So I guess it is the VDW energy. If I guess correct, you have overlapping atoms. The minimizer will mostly never get rid of such bad initial conformations. So you need to find the bad contacts (maybe using vmd and dynamic bonds with a low cutoff), or just rebuild the system. As you told you have a membrane, could it be that you have ions beside the membrane? Remember periodicity and that these ions are within the membrane then, as they get wrapped at simulation start.


Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: [] Im
> Auftrag von
> Gesendet: Samstag, 1. September 2012 08:59
> An:
> Betreff: namd-l: Error in membrane protein simulation
> 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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