[gmx-users] Stuck ...

Tsjerk Wassenaar tsjerkw at gmail.com
Thu May 24 21:14:06 CEST 2007

Hi Stephane,

If you could now send post your shoe size, your length and weight, and
pictures of worthwhile sisters if you have any, we might be able to
reinforce the incentive to help you :p

I didn't imply you were a beginner (other maybe than a beginner with
Gromacs, as you indicate yourself). I just noted that setting up HIVP
shouldn't lead to so much trouble. Now, Erik is of course right
regarding the temperatures and also with the suggestion to use
position restraints. I would like to add to that, that in most cases
it is common to perform an energy minimization in vacuum first. I
think that most of us use something like:

1. pdb2gmx
2. EM in vacuum
3. editconf/genbox/genion
4. EM in solvent (NVT)
5. EM in solvent (NPT)
6. Position Restraint MD
7. Production run

Hope it helps,


On 5/24/07, steletch at jouy.inra.fr <steletch at jouy.inra.fr> wrote:
> Selon Tsjerk Wassenaar <tsjerkw at gmail.com>:
> > Hi Stephane,
> >
> > I think this ends up in treating symptoms. Setting up a simulation of
> > HIVP should not give such problems. It's probably best to start all
> > over: pdb2gmx, EM in vacuum, editconf -d 1.0, genbox, EM in solvent,
> > etc... Keep track of everything you're doing, give all files an
> > informative name and if you do run into the same trouble, zip up the
> > log (all command lines given and the output of each program) and all
> > the files (except .xtc .trr) and make these available through the web.
> >
> > Cheers,
> And read my post ?
> Seriously, i'm not a beginner, i'm doing molecular dynamics for years using
> amber. I'm trying to figure out how precisely i can help others to have an
> updated procedure for doing a molecular md.
> My amber experience is probably not good for gromacs since the logic of using
> files is sometimes different (and it seems heating, equilibration and
> production is not used often in gromacs, probably due to the fact you can
> isolate thermal bath for different parts of the system).
> For the unix/scripting part, i'm sorry, but i don't think there is any problem
> with this. I even feel the opposite, since a script is reproducible and can
> lead to the same results all the time, but that's another story.
> Last, why not looking at my comments and see ->
> > > > http://www.steletch.org/rpm/gromacs/
> Where everything is ...
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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