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,
Tsjerk
On 5/24/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
Selon Tsjerk Wassenaar <[EMAIL PROTECTED]>:
> 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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