[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.

-Justin

> Sincerely
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



More information about the gromacs.org_gmx-users mailing list