[gmx-users] Re: pbc-replica exchange-trjconv

[Tsjerk Wassenaar]

Hoi Servaas,

Was that the trajectory for a given temperature, or for a given
system? It should be for the latter, as otherwise, there will be weird
shifts introduced. A trajectory for a given system, over the different
conditions should be (from the PBC point of view) continuous and it
should be possible to perform PBC related operations.

Hope it helps,

Tsjerk

On Thu, Jun 12, 2008 at 9:57 AM, servaas michielssens
<servaas.michielssens at student.kuleuven.be> wrote:
> Tsjerk and Justin thanks for your suggestions.
>
> Justin, the combination you suggested did not work, I tried many things
> without succes here.
> I got the following error using whole and mol. (after doing nojump)
> There were 8 inconsistent shifts. Check your topology
> There were 8 inconsistent shifts. Check your topology
> Will stop reporting inconsistent shifts
>
> Tsjerk you are right I should explain the names:
> trjconv -f gromacs.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s
> top140.tpr
>
> gromacs.trr = trajectory generated by replica exchange
> cluster.trr = output name
> lig_prot.ndx=index file of with a group for ligand and protein
> top140.tpr=tpr file generated using the starting configuration of
> gromacs.trr
>
> You were right about the fit last time, but the error stays the same if I
> don't do the fit first...
> Could the it be the fact that it is a replica exchange simulation that
> causes the problem, this makes that there are jumps in the trajectory of
> course...
>
> kind regards,
>
> servaas
>
>
>
>> 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
>>> _______________________________________________
>
>
>> Hi Servaas,
>>
>>> trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s
>>> top140.tpr
>>
>> I think there's quite a bit of reason to start calling you names here :)
>> Assumedly, fit.trr means that it results from fitting the trajectory
>> to a reference?
>> So what does this do with your PBC?
>>
>>> I also tried the -nojump option and after this the whole option but in
>>> visualistion (with VMD) I got strange bonds...
>>
>> Right, so strange bonds should be quite an indication that there's
>> something weird with your shifts.
>>
>>> 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.
>>
>> Another often, or at least several times, mentioned problem relates to
>> the fact that fitting a structure reorients the molecule, but leaves
>> the PBC as it is, causing a mismatch between the system and the PBC.
>> Therefore one can not execute any PBC related operations (nojump,
>> cluster, whole), after the trajectory has been fitted.
>>
>> No hard feelings ;)
>>
>> Cheers,
>>
>> Tsjerk
>
>>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623