From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Tue Dec 13 2016 - 23:50:53 CST
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
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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