[gmx-users] Converting trajectory into tpr file
jalemkul at vt.edu
Tue Nov 6 19:16:31 CET 2012
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.
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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