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

David van der Spoel spoel at xray.bmc.uu.se
Fri May 9 17:07:00 CEST 2003

On Fri, 2003-05-09 at 16:55, 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? Thank you very much.Leon Salgado
You will have to convert the trajectory files. THere probably exists
something that can convert dcd to e.g. Amber ascii format. Look for

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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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