[gmx-users] Converting trajectory into tpr file

Justin Lemkul jalemkul at vt.edu
Tue Nov 6 01:37:17 CET 2012

On 11/5/12 7:25 PM, rainy908 wrote:
> Fellow Gromacs users:
> Suppose I run a 1 ns equilibration on my protein system prior to molecular dynamics, and I am converting the equilibration trajectory to a TPR file.  Correct me if I'm wrong here - I'd like to confirm that I can generate a TPR file by using frames accessed in the ENTIRE trajectory, or just certain frame(s), i.e. last snapshot.

grompp does no such thing.  If given multiple frames, it uses the first frame it 
encounters.  grompp will use the last frame of a trajectory provided with -t, 
unless overridden by the -time option, in which case it uses the frame that most 
closely corresponds to that time value, per the printed documentation.

> 1. trjconv -f protein_equil.xtc -s protein_equil.tpr -o protein_b4md.gro
> 2. grompp -f md.mdp -c protein_b4md.gro -p topol.top -o protein_md.tpr
> 3. editconf -f protein_md.tpr -n index.ndx -o protein_md.pdb
> As compared to using the very last frame in the equilibrated trajectory:
> 1. trjconv -f protein_equil.xtc -s protein_equil.tpr -o protein_b4md_1ns.gro -b 1000 -e 1000
> 2. grompp -f md.mdp -c protein_b4md_1ns.gro -p topol.top -o protein_md_1ns.tpr
> 3. editconf -f protein_md_1ns.tpr -n index.ndx -o protein_md_1ns.pdb
> Does the former method output a structure that is an "ensemble average" based off of the equilibration time?  If it is indeed an average, should I use RMSD clustering to extract an actual structure accessed in the trajectory that is closest to the ensemble average?  Any suggestions would be greatly appreciated here.

There is no ensemble averaging in this protocol.  I'm not sure why you're trying 
to re-start a simulation from some arbitrary configuration during equilibration. 
  If you use some frame from within the equilibration, you'll have to start a 
new simulation from this point, which destroys the previous equilibration.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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