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 top140.tpr
The program seems to get stuck at frame 208, repeating the following lines:
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...
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,
servaas
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