[gmx-users] Re: [gmx-developers] Fwd: Simulating Gases with GROMACS 4.0

[Justin A. Lemkul]

This message is better discussed on the gmx-users list, since it is not 
pertinent to development.  I have CC'ed gmx-users at gromacs.org, and further 
discussion belongs there.

PRADEEP VENKATARAMAN wrote:
> 
> 
> ---------- Forwarded message ----------
> From: *PRADEEP VENKATARAMAN* <pvtulane at gmail.com 
> <mailto:pvtulane at gmail.com>>
> Date: Tue, Jun 2, 2009 at 5:37 PM
> Subject: Simulating Gases with GROMACS 4.0
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> 
> 
> Hi
> 
> I am trying to simulate all atom methane gas (no solvent) at 1 bar and 
> 300 K.
> 
> I minimized 300 methane molecules in 25X25X25 ang^3 box.
> 

Then I doubt you are in the gas phase.  Just because you don't have solvent 
(i.e., water) does not mean you have a gas.  This box is probably too small to 
properly describe a gaseous system, which is mostly empty space.

> When I try running at NPT simulation using the following pressure 
> coupling parameters,
> 
> Pcoupl         =       parrinello-rahman
> Pcoupltype   =       isotropic
> tau_p           =       2.0
> compressibility =   9.9e-1
> ref_p           =       1.0
> 

Posting the rest of your .mdp file is more useful.  Snippets like this hide the 
possibility that you've done something else wrong.

> I encounter the following error. Please help
> 
> ======================================================
> Step 16271, time 32.542 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.001545, max 0.019029 (between atoms 556 and 557)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     556    560   55.3    0.1113   0.1072      0.1092
>     556    557   50.9    0.1114   0.1071      0.1092
> 
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.0.5
> Source code file: constr.c, line: 136
> 
> Fatal error:
> Too many LINCS warnings (1001)
> If you know what you are doing you can adjust the lincs warning 
> threshold in your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem
> ============================================================
> 

This issue is reported frequently in the case of an unstable system, i.e.:

http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings
http://wiki.gromacs.org/index.php/blowing_up

If you want any more useful advice, you'll have to describe:

1. Your parameters (force field)
2. The full .mdp file
3. Your preparation steps (minimization, equilibration)

-Justin

> Thanks,
> 
> Pradeep
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================