[gmx-users] trjconv and -pbc

[lina]

On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Lina,
>
> Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump
>
> Hope it helps,

Hi,

Thanks.

I tried trjconv_g -fit translation -pbc nojump, ideally it should work.

but still not,

after I tried the minidist, I noticed the peak around 270ns,

I attached the figure, what's the possible reason for this distance?

Thanks,

P.S the box dimension   6.21279   6.21279   6.21279


>
> Tsjerk
>
> On Oct 28, 2011 6:27 AM, "lina" <lina.lastname at gmail.com> wrote:
>
> On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote: > Hi Lina, > > Make su...
>
> I used the initial mdrun .tpr. After checking the generated pdb (total
> 51 frames), the first 28/29 frames both are together, but later are
> separated. (the intra_fit also not work as expected).
>
> So I think at beginning the reference initial ones are together.
>
> This .xtc were trjcat together, first 200ns and then extend to 500ns,
> the .pdb generated used dt 10ns.
>>
>> Cheers,
> Am I wrong in some places? Actually for other trajectories I had no
> problem (use the same way of handling it).
>
> Thanks,
>
>> > Tsjerk > > On Oct 27, 2011 11:47 AM, "lina" <lina.lastname at gmail.com>
>> > wrote: > > Hi, > > I have ...
>
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