[gmx-users] Temperature increase

Zuzana Benkova 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).

-----Original Message-----
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.

> The 
> 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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