AW: NVT and NPT simulationd

From: Norman Geist (
Date: Wed Dec 14 2016 - 01:33:16 CST

Do you have any fixed atoms in your system?

Your system might have issues, e.g. Interlocked rings or similar. Check the minimization trajectory in VMD.

Were did you get the parameters for your polymer, are you sure they are ok?


If you want, sent your psf/pdb pair for us to check.


Norman Geist


Von: [] Im Auftrag von faride badalkhani
Gesendet: Mittwoch, 14. Dezember 2016 06:51
An: namd-l <>
Betreff: namd-l: NVT and NPT simulationd


Dear NAMD Users,

My goal is to compare the microstructure of two different polymer using MD simulations. For the first group of structures I had to perform a few steps of NVT before NPT simulations (because they did not get equilibrate well and this was your suggestion). But for the second group it is completely different because there is no problem when I run NPT immediately after minimization. But when I use the minimization+NVT+NPT I got low global count error!

I decreased the time step to 1 fs and reduced the number of processors but nothing changed. Finally, I increased the box size. In this case the NPT run is performed for about 6 ns and after that I get "Atom moving too fast" error. I read the NAMD troubleshooting and check the mentioned atom but there is nothing wrong with it.

Now I want to know how can I overcome this error?

IS there any necessity to reach equilibrium in the same way for both groups?



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