VMD-L Mailing List

From: Steven Cohen (secohen_at_mit.edu)
Date: Wed Jul 27 2016 - 07:46:38 CDT

I think you misunderstood my question. All of my simulations have the SAME
NUMBER OF ATOMS but DIFFERENT NUMBER OF FRAMES OUTPUT. I checked the log
files and this is due to VMD cutting out due to individual atoms exceeding
the per-atom velocity. I've looked through the manual and mailing list and
couldn't figure out how to address this. I tried decreasing the output
frequency but nothing changed.

Best,
Steve

On Jul 21, 2016 6:06 PM, "John Stone" <johns_at_ks.uiuc.edu> wrote:

> 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/
>