Re: [gmx-users] problem with energy minimization

[Mark Abraham]

On 31/01/2012 6:05 PM, Emanuel Birru wrote:
Yeah, Tsjerk is is right, it seems you are using 4 cpu and your system 
is too small to run in on more than one node (CPU).

If you look at the minimum required DD cell size reported by mdrun, it 
is much too large (~4nm). It is quite likely that there is problem other 
than simulation cell size.

Mark

------------------------------------------------------------------------
*From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] 
on behalf of Tsjerk Wassenaar [tsje...@gmail.com]
*Sent:* Tuesday, January 31, 2012 5:58 PM
*To:* Discussion list for GROMACS users
*Subject:* Re: [gmx-users] problem with energy minimization

Hi Anushree,

You're not using a single cpu, although you probably think you do. Is 
this em in vacuum or just a small system? Either way, you can enforce 
running on a single cpu by adding '-nt 1' to the mdrun options.

Cheers,

Tsjerk

On Jan 31, 2012 7:53 AM, "Anushree Tripathi" 
<anushritripa...@gmail.com <mailto:anushritripa...@gmail.com>> wrote:

I am using single CPU for this simulation.

On Tue, Jan 31, 2012 at 11:09 AM, Emanuel Birru 
<emanuel.bi...@monash.edu <mailto:emanuel.bi...@monash.edu>> wrote:

    > > > > From: gmx-users-boun...@gromacs.org
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