[gmx-users] RMSD of extended md

Yang Ye leafyoung81-group at yahoo.com
Mon Feb 6 15:45:31 CET 2006

You shall use same file for -s in g_rms for different trajectories. -s
denotes the reference structure.

Yang Ye

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of luigi.burgi at virgilio.it
Sent: Monday, February 06, 2006 10:27 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] RMSD of extended md

Dear Gromacs users,
i have a little problem with a rmsd calculation.
have done an 11 ns simulation and calculated the rmsd with g_rms

-s topol.tpr -f traj1.xtc -dt 2

then i extende the simulation till 30 

tpbconv -s -f -e -o tpxout.tpr -until 30000

and obtained the other 
trajectory traj2.xtc. 
Finally i calculated the rmsd for this part of 
the simulation:

g_rms -s tpxout.tpr -f traj2.xtc -dt 2

The problem is 
that when i put the two plots together the result is not contiuous.

i have to paste the two traj.xtc files together? and in that case which 
.tpr file should i use?

Thank you for any advice,

Filippo Burgi
Computational Chemistry Group
Dept. of Physical Chemistry 
- Univ. of Milan

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