[gmx-users] Re : long-term drift and crash

BON Michael michael.bon at cea.fr
Fri Aug 17 18:18:16 CEST 2007

The same bugs occurs during the NPT equilibration stage that I did after the energy minimization (with l-bgfs, till convergence), the average pressure being now -0.5 bar (over the 200 ps the simulation ran before it crashed).
Still the same things : everything I plot with g_energy is normal, the msd plot oscillates more and more, I see nothing special on the last configuration just before the crash).
This really puzzles me.
Thanks for your help.
Michaël Bon

Message: 4
Date: Wed, 15 Aug 2007 14:58:54 +1000
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] RE : long-term drift and crash
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <46C2880E.10403 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

BON Michael wrote:
> Hi and thanks,
> The pressure is stable, the mean value is -280 bar, which sounds normal, and it is isotropic (Pres-XX = Pres-YY = Pres-ZZ = -280 bar)

That value doesn't sound too normal to me, depending on the size of the 
fluctuations and the length of time over which you've measured that 
average, and/or whether the density is reasonable. Perhaps you should 
try an NPT equilibration stage as suggested here 
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation, in 
order to fix the density.

> I also tried with no constraint (I forgot to mention it in my previous mail) but it didn't solve anything.
> I did a proper energy minimization, there is no warning, error message, wierd energy at any moment. Moreover, I tried to simulate many different systems, doing each time a good minimization, and I always get this strange behaviour.


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