From: Steven Cohen (
Date: Thu Jul 14 2016 - 15:38:55 CDT

First I want to say that I was unsure if this should go to the VMD list
(for MDFF) or the NAMD list (for NAMD)

I am running several TMD simulations on the same EM map using various
initial docking positions of the same .pdb model. Other than the
orientation of the .pdb, all parameters for TMD and NAMD are the same,
specifically the number of steps and output frequency. However, when I
analyze my .dcd in VMD, each simulation has a different number of frames.
Does anyone know what could be causing this?

I am also fairly new to both VMD and MD in general, so I apologize if I
didn't include any additional pertinent information.


Steven Cohen
Graduate Student
Department of Chemistry
Massachusetts Institute of Technology