[gmx-users] problem of pr.mdp file
smayinj at nus.edu.sg
Wed Jan 2 03:04:08 CET 2008
Hi David and gmx-users,
Do you have some experience on BD using Gromacs.
I found the temperature set-up in the input must be
somewhere of half of the target temperature
(at least the output file showed like that). Other
things seem normal. Could you tell me more about this?
Thanks for your time.
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel
Sent: Tuesday, January 01, 2008 8:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] problem of pr.mdp file
> hi gmx users
> i have one doubt regarding pr.mdp file of protein.(my protein doesnt
> contain any missing residues)
> This protein i have taken after run it in amber. The steps i have done
> 1) pdb2gmx conversion
> 2) Energy minimisation in vaccum
> Now my doubt is whats the next step ? directly i will go to
> or after doing postion restrain i have to do production?
> pls anyone help me.
follow the steps in the tutorial.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before
> 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
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
gmx-users mailing list gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/search before
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
More information about the gromacs.org_gmx-users