Thank you all.
Actually I was playing with a wrong script to re-image the molecules.
Here is the one that now worked perfectly, just to keep it documented:
trajin trajectory.x
trajout trajectory.binpos binpos
center :1-10 mass
image origin center
center :1-20 mass
image center familiar
image familiar
go
At least I won't touch it anymore.... The former one suggested by Pablo
center :1-10 mass origin
image origin center
center :1-20 mass origin
image origin center familiar
brings the DNA to the border of the box, and this one keeps it at the
center. Could someone clarify it for me?
On Tue, Aug 16, 2011 at 8:07 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > There are "***" characters in the restart file. If I generate new restart
> > files from the last frame of the simulation without velocity, does it
> change
> > a lot my dynamics?
>
> It creates a new simulation - you need to do a full equilibration
> to get 'correct' velocities. The proper thing to do is probably
> re-do the last run with iwrap=1, and if you can't center your
> solute successfully using ptraj, modify ptraj or write your own
> program to center properly.
>
> Bill
>
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--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Mon Aug 22 2011 - 16:30:03 PDT
