[gmx-users] pbc-replica exchange-trjconv

[Justin A. Lemkul]

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 
> 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...
>

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 :-)

-Justin

> 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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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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