Hi Gromacs users,
I have a problem getting a snapshots using trjconv. If you could help me, I
would be very grateful. Below, I try to explain what I did and problem
happened.
Firstly, I have done 10ns long simulation (several peptides in a box). And
then, using the outputs of that simulation
On Thu, May 24, 2012 at 5:24 PM, Turgay Cakmak turgaycakma...@gmail.comwrote:
Hi Gromacs users,
I have a problem getting a snapshots using trjconv. If you could help me,
I would be very grateful. Below, I try to explain what I did and problem
happened.
Firstly, I have done 10ns long
Hi Rama,
Thanks for your quick reply.
Catenate two trajectory with help of trjcat -h
to get snapshot of particular time use trjconv -dump time
use appropriate pbc option
I have also used trjconv with -dump and -pbc nojump options, but still I
have same problem.
you are using -b 1 -e 1
Hi ,
You run extended simulation of 10 ns on your first 10ns simulation .
You get traj20ns.xtc.
these new trajectory contain all the tme frame from onwards 10ns.
So if you are giving command
trjconv –f traj20ns.xtc –s topol.tpr –b 1 –e 1 –o
snapshot20ns.gro (Note: traj20ns.xtc is
On 5/24/12 10:17 AM, rama david wrote:
Hi ,
You run extended simulation of 10 ns on your first 10ns simulation .
You get traj20ns.xtc.
these new trajectory contain all the tme frame from onwards 10ns.
So if you are giving command
trjconv –f traj20ns.xtc –s topol.tpr –b 1 –e 1 –o
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