Dear Sir, Thanks for your reply.
It means "not a number." I've never seen that before from g_energy, but > based on the extremely small error estimates, especially for the > temperature, I'd suspect you're using extremely tight coupling which may be > causing some error. I was thinking such errors come when there are some infinite values. This same mdp file parameters I have used to run 3 more simulations in different systems. But that was all fine, such "nan" error was not present. > The RMSD presented by g_energy is the standard deviation of the data > analyzed. It is unrelated to the RMSD of the protein. Yes that is true. I just checked it to make sure that there is no horrible errors in the trajectory. In a periodic system, there is no such thing as "inside" and "outside" since > the system is infinite. > Than is true. but why mentioned is that when we are analyzing we take into account only one of the unit cell not infinite. By outside I meant out of the unit cell in consideration into a periodic image. trjconv -pbc mol -ur compact (and -center if you like). Thank you I will try it out. Never used ngmx, but with the trjconv command I've stated everything should > show up quite nicely in VMD :) > Ok thanks. I am new to VMD need to explore it more. Thanking you With Regards M. Kavyashree
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