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

[PRADEEP VENKATARAMAN]

---------- Forwarded message ----------
From: PRADEEP VENKATARAMAN <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


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.

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

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

Thanks,

Pradeep
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