Chitrita Dutta Roy wrote:
Hi Tsjerk,
Did you mean to send you the md.mdp file that I used to run grompp for
md simulation? I am using Gromacs 4.0.2 versision. I am not very clear
about the parameters used in mdp files. So I am sending the mdp file here.
Some consultation with the manual will provide you with the information to learn
about these parameters. They should not be set blindly!
> cpp = /usr/bin/cpp
This is an example of one of the obsolete parameters no longer used in Gromacs
4.0.x, hence grompp told you it would be ignored.
Tcoupl = V-rescale
tau_t = 0.1 0.1
tc_grps = Protein SOL
ref_t = 300 300
Here is the problem, as grompp pointed out to you. You are controlling the
temperature of both the Protein and solvent water (SOL). But your system
contains NA+, doesn't it? So it is not part of any temperature coupling group.
Try "Protein Non-Protein" for simple aqueous systems with ions.
-Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
