[gmx-users] Re: gmx-users Digest, Vol 15, Issue 6

[Berk Hess]

>From: Brian Stephenson <bcstephe at MIT.EDU>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: RE: [gmx-users] Re: gmx-users Digest, Vol 15, Issue 6
>Date: Tue, 05 Jul 2005 10:08:59 -0400
>
>Hi Berk and Pim,
>
>Thanks for the suggestions.
>
>The first thing I thought of was that I was using my original coordinates
>and velocities too, but since my command sequence was something like:
>
>grompp -v -f eq.mdp -o eq -c int.gro -p SDSwater.top
>mdrun -v -s eq -o eq -c eq -e eq -g eq &
>
>and then later
>
>grompp -v -f eq.mdp -o eq -c eq -p SDSwater.top
>mdrun -v -s eq -o eqII -c eqII -e eqII -g eqII &
>
>there shouldn't be any way that I'd be restarting with initial coordinates 
>and
>velocities since I'm using my outputted -c file from run 1 to initialize.
>
>Also, I'm using regular, all-atomistic MD.  Could there be something in
>the dihedral transition subroutine in g_angle that I'm not understanding
>correctly?

I have no idea what this subroutine does.

You could plot some dihedral angles versus time,
(option -ov and selecting only one dihedral)
this might help you to understand what is going on.

Berk.