Re: NAMD and Gromacs

From: Francesco Oteri (
Date: Thu Sep 30 2010 - 07:55:48 CDT

If you have the latest coordinates and velocities, you need to convert
them into .gro file that can be used as restart for gromacs.

Regarding using the analysis tools of gromacs, you can use catdcd to
convert .dcd file in .trr and trjconv to convert .trr in .xtc.
When you use trjconv, you need to supply the correct timestep, because
catdcd doesn't permit to put the timestep.

The following script does the conversion:

#!/bin/tcsh -f
#Usage dcd2xtc traj.xtc timestep traj.dcd

if ( $#argv < 3 ) then
     echo "Usage: dcd2xtc output.xtc timestep traj1.dcd ..... trajN.dcd"
     exit 1

source /apps/gromacs/4.0.7/intel/bin/GMXRC
setenv SCRATCH /tmp

/apps/catdcd/4.0a/catdcd -otype trr -o $SCRATCH/traj_"$$".trr $argv[3-]
trjconv -f $SCRATCH/traj_"$$".trr -o $1 -timestep $2 <<!

If you like to extract only a part of the system, you need to modify the
trjconv invocation

On 30/09/2010 13:36, oguz gurbulak wrote:
> Dear All,
> I performed a 50 ns md simulation using NAMD and want to continue this
> simulation for 10 ns in Gromacs. Is it possible to continue a NAMD
> simulation in Gromacs ? If so, could you please give me the
> information about this process ?
> Secondly can I convert NAMD output files into gromacs output files and
> use gromacs analysis tools ? Could you please also give me the
> information about this issue ?
> Thank you very much for your attention.
> Kind regards.

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