From: Brian Radak (
Date: Thu Jun 16 2016 - 13:51:46 CDT

RMSD requires a reference structure -- most programs (I expect you are
using VMD, for example) default to using the initial configuration. Did
you inadvertently reset this between two calculations or did you repeat
the calculation for the complete 15 ns trajectory?


On 06/16/2016 12:42 PM, faride badalkhani wrote:
> Dear NAMD experts,
> I have a question regarding step by step simulations. I performed a
> NPT simulation for 10 ns and then plotted the RMSD. Then I continued
> the simualtion for 5 more ns. When I plot the RMSD for 15 ns the plot
> is decreasing decreased from 12.5 to 0.7 when it goes from first
> simulation to the second one. So, Could you give me a clue where did I
> make a mistake?
> I am sorry if it is a silly question. I am a beginner in this area.
> Regards,
> Farideh

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

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