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
>
>
>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Thu Jun 09 2011 - 07:00:03 PDT
