I don't know why you want to convert the .crd file, but you can put all
the command in only one ptraj file (i.e. converting, center, re-image,
rmsd -in that order-).
El 09/06/2011 15:47, Bruno Rodrigues escribió:
> Hi Pablo,
>
> I am converting the .crd file to binpos file and from that I run the rmsd.
>
> Should I put this command when I convert to binpos or when I run the rmsd?
>
> On Thu, Jun 9, 2011 at 10:34 AM, "Pablo I. D. Dans Puiggròs"<
> pdans.mmb.pcb.ub.es> wrote:
>
>> Hi Bruno,
>> Try this in the same ptraj run. First center the first strand, then both:
>>
>> center :1-10 mass origin
>> image origin center
>>
>> center :1-20 mass origin
>> image origin center familiar
>>
>> Good luck,
>> P.
>>
>> El 09/06/2011 15:28, Bruno Rodrigues escribió:
>>
>>> Dear all,
>>>
>>> I'm running a normal MD simulation of a 10 base pairs DNA in a water box
>>> with 8A from the last atom to the border in Amber 11.
>>>
>>> However, under the course of the simulation, part of the DNA escaped from
>>> the box and sometimes the double strand splits and one of the parts goes
>>> to
>>> the next periodic cell. It is making the RMSD to jump at ery high values.
>>>
>>> I've tried all the re-imaging commands on ptraj, like *image familiar*. I
>>> put below some of the commands I tried in *ptraj*:
>>>
>>> *1 -
>>> *
>>> center :1-20 mass origin
>>> image familiar
>>> *
>>> 2 - this is the command I'm using for running the rmsd of the backbone
>>> *
>>> trajin 1D20_wat_salt10prod.binpos
>>> image familiar
>>> rms first mass out 1D20_wat_salt10prod2.rms @P,O3',O5',C3',C4',C5' time
>>> 0.2
>>>
>>> thank you in advance
>>> *
>>> *--
>>>
>> Pablo D. Dans Puiggròs, PhD
>> Molecular Modelling& Bioinformatics Group
>> Institute for Research in Biomedicine
>> Barcelona Science Park - Spain
>> pdans.mmb.pcb.ub.es
>> pablo.dans.irbbarcelona.org
>> &
>> Biomolecular Simulations Group
>> Institute Pasteur of Montevideo - Uruguay
>> pdans.pasteur.edu.uy
>>
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Received on Thu Jun 09 2011 - 07:00:04 PDT
