Re: [gmx-users] Fwd: PMF on dihedral using Gromacs 4.04

2011-03-04 Thread Justin A. Lemkul
Joanne Martin wrote: Thanks Justin, I think I have the restraints section sorted... However, once all of the dihedrals are obtained from the MDs, I would like to do a WHAM analysis, of the reaction pathway. As I have to run each conformation as a separate MD in order to obtain all di

Re: [gmx-users] Fwd: PMF on dihedral using Gromacs 4.04

2011-03-04 Thread Joanne Martin
Thanks Justin, I think I have the restraints section sorted... However, once all of the dihedrals are obtained from the MDs, I would like to do a WHAM analysis, of the reaction pathway. As I have to run each conformation as a separate MD in order to obtain all dihedral conformations, how c

Re: [gmx-users] Fwd: PMF on dihedral using Gromacs 4.04

2011-03-04 Thread Justin A. Lemkul
Joanne Martin wrote: Hi Justin, thanks so much for the swift reply. With regards to the mdp setting > The proper setting for the "dihre" keyword is either "yes" or "no." How to I specify which dihedral I want to restrain and the force constant which I want to apply to it?? That's contr

Re: [gmx-users] Fwd: PMF on dihedral using Gromacs 4.04

2011-03-04 Thread Joanne Martin
Hi Justin, thanks so much for the swift reply. With regards to the mdp setting > The proper setting for the "dihre" keyword is either "yes" or "no." How to I specify which dihedral I want to restrain and the force constant which I want to apply to it?? Regards, Joanne On Fri, Mar 4, 2011 at 1:

Re: [gmx-users] Fwd: PMF on dihedral using Gromacs 4.04

2011-03-04 Thread Justin A. Lemkul
Joanne Martin wrote: Hi, I'm a trying to calculate the PMF of a dihedral using Gromacs version 4.04. I have read through all posts on the mailing list regarding this query, and although Chris Neale did explain how to set the restraints for Gromacs 3, these options are now obsolete for 4.04...

[gmx-users] Fwd: PMF on dihedral using Gromacs 4.04

2011-03-04 Thread Joanne Martin
Hi, I'm a trying to calculate the PMF of a dihedral using Gromacs version 4.04. I have read through all posts on the mailing list regarding this query, and although Chris Neale did explain how to set the restraints for Gromacs 3, these options are now obsolete for 4.04 I get the followi