[gmx-users] Problem with using distance restraints (disre) with PBC
s4026869 at student.uq.edu.au
Thu Mar 6 02:52:01 CET 2008
I have had a similar problem with orientation restraints.
Are the residues far is space? Are you getting inconsistent shifts? If so -
If so re-define your box size so that the shortest box vector is greater
than the distance restraint residue + some tolerance.
I also noticed -
[ distance_restraints ]
;ai aj type index type low up1 up2 fac
9 413 1 0 1 8.18 8.18 10.0
Have you defined the low up and up2 in the correct units?
TJ Piggot wrote:
> Firstly I would strongly reiterate what Mark said. I would make sure
> the distance restraints are causing your problem. Again as Mark said
> make sure you can simulate your system without the distance
> restraints, and then I would try to simulate the system with distance
> restraints and with a much larger box of water surrounding your
> peptide. Here you should also be able to overcome the problem (if it
> is this problem) with a large enough distance between periodic images.
> If you can then confirm what you have suspected to be the problem you
> will need to modify the source code slightly. If you search the list
> (searching for "inconsistent shifts using multiple bonds type 6") you
> can see the changes you need to make, as suggested by Berk Hess to me
> when i had this problem with bond type 6.
> Hope this helps
> --On Wednesday, March 05, 2008 17:16:23 -0500 Grace Li
> <fullofgrace88 at gmail.com> wrote:
>> I am having some trouble using distance restraints. My goal is to
>> apply a
>> harmonic potential to the distance between two atoms in a short peptide
>> (35 residues). Doing simulations in vacuo, both of the following
>> techniques worked to restrain the distance. Also, both techniques worked
>> for simulations in water without periodic boundary conditions. As soon
>> as I include pbc = xyz in my .mdp file and use PME for the
>> electrostatics, my simulation crashes (producing step0.pdb and
>> step-1.pdb). I am assuming this is because GROMACS is using the distance
>> to the image of the other atom, not the actual distance in the box? Is
>> there any way of getting around PBC for distance restraints?
>> Specifically, I have used the following:
>> 1. I have tried using bonds type 6 in my topology:
>> [ bonds ]
>> ; ai aj funct c0 c1 c2 c3
>> 9 413 6 8.18 421.54
>> 2. When using distance restraints, I added the following lines to my
>> topology file:
>> [ distance_restraints ]
>> ;ai aj type index type low up1 up2 fac
>> 9 413 1 0 1 8.18 8.18 10.0
>> In the case of using [ distance_restraints ] in the topology file, I
>> added the following lines to my .mdp file:
>> disre = simple
>> disre_fc = 421.54
>> disre_weighting = equal
>> disre_tau = 0
>> (and various other values of the force constant, disre_fc, but in all
>> cases the run crashes).
>> Thanks for any suggestions!
>> 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
> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
> 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