Hi,
I am sure what exactly you are trying to simulate, but your distances
seem a bit large (8.1 nm) for a small peptide. Having your restraints
_far_ off may cause a crash.
Flemming
On 5 Mar 2008, at 17:16, Grace Li 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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