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
*
*--
--
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 - 06:30:03 PDT
