[gmx-users] RMSD of extended md

[Xavier Periole]

luigi.burgi at virgilio.it wrote:

>Dear Gromacs users,
>i have a little problem with a rmsd calculation.
>I 
>have done an 11 ns simulation and calculated the rmsd with g_rms
>
>g_rms 
>-s topol.tpr -f traj1.xtc -dt 2
>
>then i extende the simulation till 30 
>ns
>
>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.
>
>Do 
>i have to paste the two traj.xtc files together? and in that case which 
>.tpr file should i use?
>
>  
>
You have to use the same reference for the two rmsd of the trajectories ...
the first rmsd is ok, the second uses (tpxout.tpr) the conformation that was
used for the continuation run ... not good.

you got to do g_rms -f traj1, 2, 3, 4, 5.xtc -s topol1.tpr

XAvier

-- 
----------------------------------
 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 
 Tel: +31-503634329
 Fax: +31-503634398
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole
----------------------------------