I had many problems with imaging as well. Make sure you use the wet
trajectory, if you want to have as well the trajectory without waters,
remove them after the image/center commands.
Good luck, Nadine
On 06/09/2011 03:53 PM, "Pablo I. D. Dans Puiggròs" wrote:
> 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 - 07:30:03 PDT
