Hi,
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
Cheers
Tom
--On Wednesday, March 05, 2008 17:16:23 -0500 Grace Li
<[EMAIL PROTECTED]> wrote:
Hello,
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
1.0
In the case of using [ distance_restraints ] in the topology file, I
have
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!
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----------------------
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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