On 7/12/2011 7:41 PM, lloyd riggs wrote:
Message: 3
Date: Tue, 06 Dec 2011 18:58:50 +0100
From: Javier Cerezo<[email protected]>
Subject: Re: [gmx-users] RE: logfile size
To: Discussion list for GROMACS users<[email protected]>
Message-ID:<[email protected]>
Content-Type: text/plain; charset=UTF-8; format=flowed
Not the main problem, but your dt=0.0002 (0.2fs), is it what you want?
Javier
Yeah,
I found when you have 10,000 + protein atoms + assorted others (2 different
ligands of say 5000K atoms) the time steps have to remain smaller or you start
getting problems with all sorts of things from Temp coupling to simple
integrations between steps. I can EQ it at 0.02, for 1M steps or more, and
still run into the same problem when I switch to MD integrators. Dont know if
this is universal though, as I spent time making sure the models are correct,
ie error free after EQ's (em, NVT, NPT). They run though fine at that time
step, it just makes the whole simulation take a while to run, as time steps
translate into direct computational time.
Post-equilibration MD at normal T and P with all bonds constrained
should be stable with 2fs time steps. If not, then I'd say there's
something wrong with the parameters and a smaller time step is not
actually a fix.
Mark
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