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