[gmx-users] NVT equilibration

[Peter C. Lai]

On 2012-08-09 05:56:46AM -0700, Shima Arasteh wrote:
> 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?

So the system crashed before LINCS did. Perhaps more energy minimization
would be helpful? See what atoms/residues were misbehaving (when LINCS
throws those errors, it gives you the atom #) and look at its neighbors to
see what sort of large forces might arise.

> 
> Am I supposed to change the rcoulomb and rvdw cutoffs? How would I be sure of a correct changes? 
> 

You are supposed to use the cutoffs appropriate for your forcefield.

> 
> Sincerely,
> Shima
> 
> 
> ----- Original Message -----
> From: Peter C. Lai <pcl at uab.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: 
> 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? 
> > 
> > 
> > Cheers,
> > Shima
> > -- 
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> -- 
> ==================================================================
> Peter C. Lai            | University of Alabama-Birmingham
> Programmer/Analyst        | KAUL 752A
> Genetics, Div. of Research    | 705 South 20th Street
> pcl at uab.edu            | Birmingham AL 35294-4461
> (205) 690-0808            |
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-- 
==================================================================
Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|
==================================================================