[gmx-users] NAMD2/VMD vs Gromacs analysis tools

Andrea Bernini andrea.bernini at unisi.it
Sat May 10 10:05:01 CEST 2003

Leon Salgado wrote:
> Hello all gmx's
> In my lab we started to perform MD simulations with the NAMD2 pack.
> VMD is a program from the same group, used to display the trajectories 
> and by using some Tcl and Phyton scripts, we can do "some" post MD analysis.
> But, in my opinion, the tools available are "few".
> Heard about another GPL software, GROMACS, that in addition of doing MD, 
> as already several analysis tools implemented.
> In the meanwhile (thinking in migrating to gmx), we want to try analyse 
> our NAMD2 results within GROMACS, if this is possible. The relevant 
> files to analyse trajectory inside namd2, are a binary trajectoryfile, 
> .dcd , and a .psf file describing the molecular structure.
> Is it possible to analyse my namd2 runs in GROMACS?
Yes, but you have to convert the .dcd trajectory into gromacs .trr 
format first by using the trio software, that can be found among the 
MDtools (http://www.ks.uiuc.edu/Development/MDTools/, the same site 
where you found NAMD and VMD). The .psf file can be converted by using 
babel. Note also that NAMD can now accept gromacs input files, so you 
can use a combination of the two.

Ciao, Andrea

> Thank you very much.
> Leon Salgado
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Andrea Bernini, D. Phil.
Molecular Biology Dept.
University of Siena

e-mail: andrea.bernini at unisi.it

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