This message is better discussed on the gmx-users list, since it is not
pertinent to development. I have CC'ed [email protected], and further
discussion belongs there.
PRADEEP VENKATARAMAN wrote:
---------- Forwarded message ----------
From: *PRADEEP VENKATARAMAN* <[email protected]
<mailto:[email protected]>>
Date: Tue, Jun 2, 2009 at 5:37 PM
Subject: Simulating Gases with GROMACS 4.0
To: [email protected] <mailto:[email protected]>
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
========================================
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