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

Brian Stephenson bcstephe at MIT.EDU
Tue Jul 5 16:08:59 CEST 2005

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


At 03:42 PM 7/5/2005 +0200, you wrote:

>>From: Pim Schravendijk <schraven at mpip-mainz.mpg.de>
>>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>To: gmx-users at gromacs.org
>>Subject: [gmx-users] Re: gmx-users Digest, Vol 15, Issue 6
>>Date: Tue, 5 Jul 2005 14:59:46 +0200 (CEST)
>> > Date: Mon, 04 Jul 2005 11:18:54 -0400
>> > From: Brian Stephenson <bcstephe at MIT.EDU>
>> > Subject: [gmx-users] restarting runs
>> >
>> > Hi all,
>> >
>> > ...
>> >
>> > I've  noticed things like this using GROMACS before--when I restart runs
>> > using my old output as my new starting point,
>> > the initial behavior seems unequilibrated.
>> >
>> > ...
>> >
>> > Any suggestions will be much appreciated!
>> >
>> > Thanks,
>> > Brian
>>Do you use pressure coupling? It might have to do with your coupling
>>starting unequilibrated.
>>You coulda avoid this by, when you restart a run, doing this by using
>>tprconv and use the last complete frame from your .trr file and .edr file.
>I don't think this it the problem.
>It would only have a very minor effect on the system,
>which you can not observe directly, only by comparing with an exact
>continutation run.
>My first guess would be that the same starting coordinates or velocities
>have been used.
>And it the simulations true md, or sd or bd?
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