[gmx-users] "Justifying" 4fs production runs after 1fs equilibrations?

unitALX alec.zander at gmail.com
Tue Feb 11 12:12:06 CET 2014

Helllo all!

In my general situation, I have a batch of homology models that I would like
to assess for stability by molecular dynamics. 

I am working with a postdoc in my lab who was extensive experience with
NAMD, but does not use GROMACS. We have been developing protocol for these
MD simulations, but we had some different views on equilibration and

My friend is recommending that I do equilibration for 500ps @ 1fs with no
constraints. I have no real objection to that, but he made it seem like the
results might be quite different than an equilibration for 200ps @ 2fs with
LINCS all-bonds. Would it make a critical difference?

I was excited by the performance possible with LINCS all-bonds, -vsite
aromatics @ 4fs, but my friend looks at 4fs with disgust. I responded with
arguments from the GROMACS 4 paper, and a paper called "Improving efficiency
of large time-scale molecular dynamics simulations of hydrogen-rich systems"
re: the relationship between the period of the fastest vibration and largest
allowable timestep, but he seems quite convinced that for publication, only
1fs and possibly 2fs production runs (preferably without barostat and
thermostat??) are acceptable. The suggestion to drop the barostat and
thermostat for production follows the philosophy that if your minimization
and equilibration is properly done, then the system should be stable in
production without pressure & temperature control. I'm having a hard time
finding better literature "justifications" for usage of LINCS all-bonds @
2fs, and certainly for -vsites @ 4fs; P&T control seems quite standard in
publications using GROMACS.  Can you suggest any papers or calculations I
can do to show the validity of these options?

View this message in context: http://gromacs.5086.x6.nabble.com/Justifying-4fs-production-runs-after-1fs-equilibrations-tp5014461.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list