[gmx-users] Converting trajectory into tpr file

[rainy908]

I was making a clarification regarding the equilibration, not the RMSD clustering.

On 6 November 2012 10:16, Justin Lemkul <jalemkul at vt.edu> wrote:


On 11/6/12 1:14 PM, rainy908 wrote:
I wasn't outputting an "arbitrary" configuration - the timestep at 1000 was the last frame of my equilibration.


I was replying to your question regarding the choice of configuration, whether or not you needed to do any sort of RMSD clustering.

-Justin


On 5 November 2012 16:37, Justin Lemkul <jalemkul at vt.edu> wrote:


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


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

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

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