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 <[email protected]> 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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