VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 21 2016 - 17:05:49 CDT

Hi,
  In your case, I think that that fundamental question is to find out why
you have a differing atom count between your various files.
Once you answer that question and use files with consistent structural content,
VMD will be more cooperative. Without knowing what specific steps you
performed however, nobody would be able to guess how you ended up with files
that contain non-uniform numbers of atoms.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 14, 2016 at 04:38:55PM -0400, Steven Cohen wrote:
> 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.
> Best,
> Steve
> --
> Steven Cohen
> Graduate StudentA
> Department of Chemistry
> Massachusetts Institute of Technology
> [1]secohen_at_mit.edu
>
> References
>
> Visible links
> 1. mailto:secohen_at_mit.edu 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/