[gmx-users] Re: MDS of transmembrane protein

Anton Feenstra feenstra at few.vu.nl
Thu Jan 19 15:48:43 CET 2006

Vandana Kumari wrote:
> Dear Sir,
> I want to do molecular dynamic simulation of transmembrane protein of
> residue 309. The 3D structure of that protein is not known. I have
> modelled that protein by homology now I want to do Molecular dynamic
> simulation of that transmembranne protein. Is it possible to do simulation
> by GROMACS? Please suggest me system requirement for the MDS of
> transmembrane protein of residue 309.

Generally speaking, MD of membrane proteins is not very easy. But, yes, 
it is possible to do, and, yes, you can do it with GROMACS. However, I 
am not an expert in membrane protein simulations. What I do know, is 
that a system of a protein(-complex) plus membrane plus water (solvent) 
typically is large (>50000 atoms). On a single high-end (~3.5GHz) 
pentium CPU, you would probably require several days, or maybe even more 
than a week, for a single nanosecond. In addition, you will first have 
to equilibrate your system, which can be also very difficult and 
time-consuming... I don't want to scare you, but I also don't want to 
give you unrealistic expectations.

One of the best places to start, would be the website of Prof. Peter 
Tieleman: http://moose.bio.ucalgary.ca/. He is one of the pioneers of 
membrane protein simulation, and also uses Gromacs a lot.

Also, do have a look in the archives of the Gromacs Users mailing list:
Searching for 'membrane protein' should get you some additional 
pointers, and solutions to problems you might run into. Be aware that if 
you want to post a message to the list, you will first have to subscribe 
(which you can do online).



* NOTE: New Affiliation, Phone & Fax numbers (below) *
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam   |
|(   |   )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands  |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |

More information about the gromacs.org_gmx-users mailing list