[gmx-users] a question about analysis

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 2 18:05:42 CET 2009

oguz gurbulak wrote:
> Dear All,
> I converted the mdcrd ( coordinates, box sizes ) and mdvel ( velocities 
> )  Amber trajectory files for every md record into the pdb format using 
> ptraj in Amber. Can I use these pdb files in Gromacs for performing 
> analysis ? Or Will I need to have some extra files to use analysis 
> programs of Gromacs ? I will only use g_msd , g_velacc , g_energy for 
> calculating viscosity. I'm waiting for your advices.

Some options within the analysis tools require a .tpr file (binary input for a 
Gromacs simulation).  It depends on what you are trying to do.  g_velacc 
requires a .trr trajectory file as input (produced from a simulation), so .pdb 
will not work.  g_energy requires a .edr file (also from a simulation).

For investigating what tools do and what you need to give them, read the help 
information from the -h flag for each tool.


> Sincerely
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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