[gmx-users] a few questions

[Anton Feenstra]

Robert Soliva wrote:

> Hi all GROMACS fans.
> 
> I am a new user starting from scratch with the program. I would like to
> ask you all a few questions.
> Sorry if they seem to obvious/stupid.
> 
> 1- What tutorials do you recommend for easy and quick learning of the
> program, other than the getting started examples of your web site?

There must be some. IIRC, there are a few pointers in the Links. 
Otherwise, have you tried google?

> 2- I was wondering if there are any papers on the use of GROMACS for
> simulating GPCRs in a lipid bilayer. Do you know of any such papers?

A coleague of mine has done some of these. I'll ask him (though, he is 
on the list as well)...

> 3- Is there an easy way for converting GROMACS files to (and from) other
> standard MM/MD packages such as AMBER and CHARMM?

For coordinates, use .pdb files (or use awk to convert Amber crd files 
to Gromos .g96 files to prevent loss of precision, and include velocities).

For topologies, there are some scripts on the contribution pages, but to 
my knowledge they have not been tested. Use with care and discretion!


-- 
Groetjes,

Anton

* NOTE: New Phone & Fax numbers (below) *

  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
|_____________|_______________________________________________________|