Re: How to continue RMSD of previous production simulation

From: Chitrak Gupta (
Date: Fri Dec 02 2016 - 12:43:05 CST

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 <>

> 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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