[gmx-users] Recommended way to run production using the same conditions as equilibration

[Andrew DeYoung]

Hi,

In molecular dynamics I have learned that there are three main phases:
energy minimization, equilibration (say, 2 ns in duration), and
production/dynamics (say, 3 ns in duration).  Suppose that I want my
production run to use the same conditions as equilibration.  What is the
best way to do this?

I can think of two conceptual ways to approach this:
(1) Do one long 5 ns run.  Then, when doing analysis, ignore the frames
corresponding to the initial 2 ns, using the -b option found in most of the
Gromacs trajectory analysis programs to consider only the final 3 ns.

(2) Do equilibration and production in separate runs.  This way, doing
analysis is perhaps more foolproof:  I don't need to worry about always
neglecting the initial 2 ns, and the initial time I consider is always,
conveniently, t = 0 ps.  

>From looking at various Gromacs tutorials, it seems that approach (2) is
recommended.  But now, even within approach (2), there are at least two
options.  One option is to feed the checkpoint file from equilibration into
the grompp part of production.  For example, 

EQUILIBRATION: 
[equilibration has been prepared using grompp]
mdrun -deffnm npt-eq -cpo npt-eq.cpt
PRODUCTION:
grompp -f npt-md.mdp -c npt-eq.gro -t npt-eq.cpt -p water.top -o npt-md.tpr
-po npt-mdout.mdp
mdrun -deffnm npt-md

where I have used the -cpo option in mdrun of equilibration and fed this
resulting checkpoint file to grompp of production, using -t.  Is this
correct?

Or, I could eliminate the grompp step of production (since my production run
uses the same parameters as in equilibration) and feed the checkpoint file
directly to mdrun of production:

EQUILIBRATION: 
mdrun -deffnm npt-eq -cpo npt-eq.cpt
PRODUCTION:
mdrun -deffnm npt-md -cpi npt-eq.cpt

where I have used -cpi in mdrun of production to feed in the checkpoint
file.  (In contrast to grompp, there is no -t option in mdrun.)  Is this
correct?  My concern here is that, in the entry for mdrun in the Gromacs
manual, it says that for the option -cpi, "By default the output will be
appending to the existing output files."  But since I have specified output
file names using -deffnm npt-md, will the trajectory indeed be written to
npt-md files, or will it be appended to the npt-eq files, from which the
checkpoint file originated?  

If both of these options are correct, which is preferable?

Thank you very much.

Andrew DeYoung
Carnegie Mellon University