Hi i have modified the src to stop harmonic potentials being put into the
graph (as was suggested to me by Berk Hess, see below for the modification
you need to make). I would be imagine this is also possible to do for
distance/orientation restraints, however i only know a small amount of
programming so you will need someone else to help you here. Here is the
change i have made and it works fine for me:
A real fix would then be adding
i!=F_HARMONIC &&
to the if statement on line 272 of src/gmxlib/mshift.c
and recompiling Gromacs, such that the harmonic potentials
are not put into the graph.
Tom
--On Thursday, March 06, 2008 12:50:18 +1000 Mitchell Stanton-Cook
<[EMAIL PROTECTED]> wrote:
Hi Tom,
Have you modified the src? As far as I know this has not been done in 331
or 332. I'm unsure of 333. I would be interested in the patch. As far as
I know the problem is due to the the distance/orientation restraints
being placed in the bonded graph. There was a bit of chatter on the
developers list in 2007 about this but I haven't heard much else.
For my system I was using a truncated dodecahedron box. The box vector
1/2d was my biggest problem. I simply changed to a triclinic box without
too much cost. However I think I could grab an extra 300ps/day if I had
an actual fix.
Cheers
Mitch
TJ Piggot wrote:
I agree with increasing the size of the box (if seeing inconsistent
shifts, as i should have mentioned in my previous post) and in this
case it is practical to do as the system is quite small. However (just
for future reference) if the problem were in a much larger system (as
it is in my case) then it may be more suitable to modify the source
code to avoid increasing the size of the system simulated.
Tom
--On Thursday, March 06, 2008 11:52:01 +1000 Mitchell Stanton-Cook
<[EMAIL PROTECTED]> wrote:
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
1.0
Have you defined the low up and up2 in the correct units?
Cheers
Mitch
TJ Piggot wrote:
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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[EMAIL PROTECTED]
University of Bristol, UK.
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[EMAIL PROTECTED]
University of Bristol, UK.
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[EMAIL PROTECTED]
University of Bristol, UK.
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