Andrew DeYoung wrote:
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.
If the conditions for equilibration and production are identical, then either
approach works. Most workflows separate equilibration and production due to the
use of restraints, different T or P coupling schemes, etc. But if all you're
doing is extending the same ensemble, then the choice here between 1 and 2 makes
no difference.
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?
Yes. See, for instance:
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Changing_.mdp_file_options.
and
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation
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?
They will be written to npt-md.xtc/log/etc. When supplying -deffnm, the use of
any other flag for input or output overrides the name in -deffnm, so you can use
the previous checkpoint file, even if it has a different name. You can also get
around the appending problem by using -noappend.
If both of these options are correct, which is preferable?
Whichever one makes sense to you. I tend to go with the grompp/mdrun combo.
That offers you the ability to change .mdp options for I/O purposes, remove
restraints, etc.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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