[gmx-users] NVT equilibration
shima_arasteh2001 at yahoo.com
Thu Aug 9 14:56:46 CEST 2012
Thanks for replies.
Some bonds are rotated more than 30 degrees ,as it's written just before turning off the equilibration.
Is this over-rotation also included in interaction with PBC images?
Am I supposed to change the rcoulomb and rvdw cutoffs? How would I be sure of a correct changes?
----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, August 9, 2012 5:08 PM
Subject: Re: [gmx-users] NVT equilibration
Parts of your system shifted too much (in Y dimension) for PME to handle.
What happens to the system up to the point of the crash?
How large is the system (particle count) vs. # of PME nodes used?
Could be your system is too small for the # of PME nodes used
Is the protein somehow interacting with its own PBC images? Is there enough
water in the box to shield the protein from seeing itself in the next box
over - it's probably safe to go with a thickness of water around the protein
that is equal to the rcoulomb and rvdw cutoffs (that way you really get 2x
the distance between protein images).
On 2012-08-09 05:23:17AM -0700, Shima Arasteh wrote:
> Dear gmx users,
> I used the NVT (T=300) equilibration for my system ( a protein in water). The first time, I set 100 ps for system for equilibration, It resulted in RMSD=3.96 with an average temperature around 299.803 K.
> Then I though of a better convergence, so set the equilibration to 200 ps. But it stopped due to some error:
> Fatal error:
> 1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.
> This usually means that your system is not well equilibrated.
> I'd like to know why such an error might happen? Is a shorter equilibration better for NVT generally?
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Peter C. Lai | University of Alabama-Birmingham
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