[gmx-users] Temperature increase
upolzben at savba.sk
Fri May 4 14:36:32 CEST 2007
Dear Mark, thank you very much for prompt reply, I am sorry but I did
mistake in my first e-mail I have run an NVE simulation of decamer of glycin
first with PBC (coulombtype=PME)and later without PBC (coulombtype=Cut-off).
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Mark Abraham
Sent: Thursday, May 03, 2007 3:46 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Temperature increase
Zuzana Benkova wrote:
> I have run an NVE simulation of decamer of glycin first with PBC
> (coulombtype=Cut-off) and later without PBC (coulombtype=PME).
You can't have a non-periodic system with PME.
> gen-temp was set to 300K with option gen-vel=yes. The temperature start
> to raise during simulation and finaly the following messages appeared in
> log file
> Shake did not converge in 1000 steps
> i mi j mj before after should be
> 66 14.01 67 1.01 0.10100 0.10318 0.10100
> Constraint error in algorithm Shake at step 980454
> Wrote pdb files with previous and current coordinates
> How can I cope with this?
We can't tell, because the above description is not self-consistent.
In any case you haven't defined your topology, or minimized your
structure or equilibrated properly. Then some bad structural element is
causing a region to have too much energy which is breaking structures.
Search the mailing list archives for suggested equilibration regimes, or
read relevant literature examples, or do tutorial material.
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