[gmx-users] pbc-replica exchange-trjconv
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 11 15:39:32 CEST 2008
servaas michielssens wrote:
> Dear gromacs users,
> I have a problem that is already discussed a lot on the mailing list,
> in a protein-ligand simulation the ligad jumps out of the box. The
> trajectory is generated by replica exchange simulation. So I used
> trjconv with the option cluster:
> trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s
> The program seems to get stuck at frame 208, repeating the following
> COM: 1.730 1.730 2.447 iter = 6214 Isq = 21.428
> COM: 0.000 0.000 0.000 iter = 6215 Isq = 54.757
> COM: 1.730 1.730 2.447 iter = 6208 Isq = 21.428
> COM: 0.000 0.000 0.000 iter = 6209 Isq = 54.757
> COM: 1.730 1.730 2.447 iter = 6210 Isq = 21.428
> COM: 0.000 0.000 0.000 iter = 6211 Isq = 54.757
> COM: 1.730 1.730 2.447 iter = 6212 Isq = 21.428
> if I use this command:
> trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster
> The program runs but the ligands is still out of the box, the option
> -s seems to be necessary, but not working in my case.
> I also tried the -nojump option and after this the whole option but in
> visualistion (with VMD) I got strange bonds...
I've found that sometimes several iterations of trjconv are necessary to
get such things fixed up. Something like -pbc nojump, followed by
'whole,' and 'mol' or 'res' after that might do the trick. It's a bit
of trial and error, and if anyone else out there has a better method,
I'd love to hear it, too :-)
> An often reported problem was that the the structure in the tpr file
> is not close enough to the starting structure in the trajectory, I
> tried it by making a tpr file with a the strating structure of the
> trajectory (in this structure the ligand is in the active site if I
> look at the structure). But this did not help.
> What I am doing wrong here?
> thanks in advance for your help!
> kind regards,
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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