[gmx-users] R: Md continuation with cpt

Anna Marabotti anna.marabotti at isa.cnr.it
Thu Apr 28 16:55:09 CEST 2011

Dear Mark,
thank you very much for your hint. It's a relief to know that I haven't to
redo the simulation!
>From now on I will set init_step = 0 for my simulations.


Message: 3
Date: Thu, 28 Apr 2011 20:56:00 +1000
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] R: Md continuation with cpt
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4DB947C0.90702 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 4/28/2011 5:47 PM, Anna Marabotti wrote:
> Dear Justin,
> thank you for your precious help. Yes, the problem is what you say and
> I was suspecting too (but I was not sure, that's why I was searching for a
> confirmation of my suspects from more expert people). The problem however
> present in the NVT->NPT junction. My .mdp settings were
> NVT:
> tinit = 0
> init_step = 0
> nsteps = 10000
> dt = 0.002
> tinit = 0
> init_step = 20000 (instead of 10000)
> nsteps = 50000
> dt = 0.002
> That's why I had a last NPT step of 70000 instead of 60000, and that's why
> set init_step = 70000 in the production MD.
> What you are saying also explains the anomalous behaviour of the xvg file
> created from the .edr file, in which only few points were saved, therefore
> the graphs created with xmgrace contain only 7 values (at 140, 200, 300
> 5140, 10140, 15140 ps).
> I always set nstep identical to the last step of the previous
> MD because I understood that it was necessary to do it to obtain an exact
> continuation, there is no other special reason.

The label on the step number has nothing to do with the physics. 
Instructions for restarts preserving simulation ensembles are on the 
website. IIRC init_step refers to the label given to the step whose time 
is tinit (see manual 7.3.3), and haphazardly changing only one of them 
might lead to such problems.

>   Since you are saying that
> this is no (longer?) necessary (I'm currently using Gromacs 4.0.7 on this
> machine), I'm very happy to set always nsteps = 0, to avoid future

Do that.

> In the meantime, what I have to do? I had a look at the .xtc files with
> gmxcheck and apparently all is fine, with no error messages, also the
> trajectory seems to be coherent with my expectations. I run g_rms and
> g_gyrate and the behaviour of the systems appears "normal" (apart from the
> fact that the system is not stabilized yet, so I have to continue the
> trajectory). I can provide you (offlist) the .xvg graphs, if you want.
> Based on these data, what do you suggest to do? Do you think that the
> simulation could be considered formally correct (i.e. this is only a
> of erroneous writing of .edr file) or do I have to repeat
> (AAAAAARRRRRRGGGGHHHHH) the whole simulation? I saw in the manual that the
> option -rerun of mdrun command allows to recalculate forces and energies
> from a trajectory file, do you think that I can use it to obtain a new
> file?

If it's just a problem of labelling the frames, then trjcat and eneconv 
have -settime to deal with these kinds of scenarios.


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