AW: How to continue RMSD of previous production simulation

From: Norman Geist (
Date: Sat Dec 03 2016 - 05:51:18 CST

Ok sry for the confusion. Your question was related to the problem, that you have frames in your DCD files that have been written there, after the last restart files have been created, from which you later restarted. Therefore you have some jumps in your RMSD from DCD file to DCD file. The easiest option here is to truncate the DCDs to the last timestep where a restart file have been written, so there are no redundant frames. This can be done using e.g. catdcd.


Norman Geist


Von: [] Im Auftrag von Chitrak Gupta
Gesendet: Freitag, 2. Dezember 2016 19:43
An: NAMD list <>; Farhad Jahanfar <>
Betreff: Re: namd-l: How to continue RMSD of previous production simulation


Hi Farhad,


How are you calculating RMSD? Are you using VMD's RMSD plugin, and are you doing it separately for each trajectory? Note that by default, VMD calculates RMSD with respect to the first frame that you have loaded (as far as I know). So, if you are loading the trajectories separately each time, then the reference frame is changing each time. If you load all your trajectories together then you should see a consistent RMSD.



Hope this helps.



On Fri, Dec 2, 2016 at 1:21 PM, Farhad Jahanfar < <> > wrote:

Dear NAMD users


I want to run my production simulation in separate runs.

For example, instead of 10 ns simulation i want to run it in 5 simulations in 2 ns.

I know how to use restart files and continuing, but my problem is RMSD of each simulation which does not starts from where the previous run ends, and i couldn't put RMSDs together like there is no stop between runs.

I think it must be common problem for long time simulations like >1000 ns.

Is there any script that could help?


Best regards


Farhad Jahanfar


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