[gmx-users] Re: Targeted MD

wei-xin xu xwxnju at gmail.com
Thu Jan 10 03:28:09 CET 2008

2008/1/10, Mark Abraham <Mark.Abraham at anu.edu.au>:

> Stanislav Bobritsky wrote:
> >      > Well, but (as I know from Manual, Ch. 6, p. 120) there is
> >     "approach to do targeted MD" in GMX.
> >
> >     Did you add position restraint to your protein
> >     topology?
> >
> >
> > No, I did not.
> > What group must be restrained therefore? Whole protein or whole protein
> > except loop?
> From "man grompp",
> > When using position restraints a file with restraint coordinates can be
> > supplied with -r, otherwise restraining will be done with respect to the
> > conformation from the -c option. For free energy calculation the the
> > coordinates for the B topology can be supplied with -rb, otherwise they
> will
> > be equal to those of the A topology.
> Thus I expect your earlier grompp command line didn't do the job you
> thought it did.
> You could restrain just the loop if you knew the protein was stable, but
> easiest is to present conformation A as -c and B as -r. pdb2gmx will
> have supplied you with a posre.itp file, and you need -DPOSRES in the
> include .mdp directive so that the former works.
> Your .mdp file as supplied earlier should not T-couple only your solute,
> and neither should it couple your counterions separately from the
> solvent. See http://wiki.gromacs.org/index.php/Thermostats

Some hints on practices that generally *not a good idea* to use:

   - Do not use separate thermostats for different components of your
   system. Some molecular dynamics thermostats only work well in the
   thermodynamic limit. If you use one thermostat for, say, a small molecule,
   another for protein, and another for water, you are likely introducing
   errors and artifacts that are hard to predict. In particular, do not couple
   ions in aqueous solvent differently from that
   - solvent.

Sorry that I do not actually understand here. The link I copied above shows
that better not to "couple ions in aqueous solvent differently from that
solvent". Maybe not separately but differently (mean different temperature)?

I am actually a novice in Gromacs.

> Based on the foregoing, I'd guess that you're fairly new to MD and/or
> GROMACS. I'd strongly recommend doing some (more) tutorials and
> background reading so that you have more idea what "normal" MD is, and
> the consequences of changes you might make. Otherwise the odds are
> excellent you're just using an complicated quasi-random number generator.
> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080110/179cfd39/attachment.html>

More information about the gromacs.org_gmx-users mailing list