On 2/8/13 9:12 AM, Shima Arasteh wrote:
Doesn't that mean the npt should be done for a longer time?
No. Look at the snippet of the .log file - the temperature at step zero is >
1800K! That indicates that the system is wildly unstable from the very start.
Solutions to the problem are suggested in the link Mark provided, which have
also been posted thousands of times to this list ;)
-Justin
From: Mark Abraham <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Sent: Friday, February 8, 2013 5:37 PM
Subject: Re: [gmx-users] Reg:1 particles communicated to PME node 0 are more
than 2/3 times the cut-off
On Fri, Feb 8, 2013 at 7:48 AM, Subramaniam Boopathi
<[email protected]>wrote:
dear sir,
how can i remove this following problem
Energies (kJ/mol)
Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
2.36059e+03 3.53976e+02 7.34586e+00 7.00084e+03 2.02621e+03
LJ (SR) Coulomb (SR) Coul. recip. Position Rest. Potential
7.70414e+03 -5.91044e+04 -6.76092e+03 1.80260e+00 -4.64104e+04
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
6.48550e+04 1.84446e+04 1.84446e+04 1.88479e+03 7.32453e+03
Constr. rmsd
4.81184e-01
-------------------------------------------------------
Program mdrun_d, VERSION 4.5.5
Source code file: pme.c, line: 538
Fatal error:
1 particles communicated to PME node 0 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.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Did you try following the link mdrun suggested? :-)
Mark
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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