[gmx-users] pbc-replica exchange-trjconv

[servaas michielssens]

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