On 5/13/12 9:11 PM, Andrew DeYoung wrote:
Greetings,
I am running 5 ns of equilibration followed by 10 ns of production dynamics.
Equilibration and production dynamics differ only in the number of steps and
the frequency of saving the positions, velocities, forces, and energies. To
conserve disk space, I set nstxout = nstvout = nstfout = nstenergy to some
high value, such as 1000000 (in equilibration.mdp), for equilibration. Then
You can set them to zero to completely eliminate output, if you need to.
for production dynamics, I set nstxout = nstvout = nstfout = nstenergy to
some relatively low value, such as 100 (in dynamics.mdp), because it is from
these data that I will do property analysis.
So, to do this, I have been using a workflow like this:
(1) For equilibration, feed equilibration.mdp to grompp using "-f". Then
run mdrun, saving the checkpoints to state.cpt.
(2) For production dynamics, feed dynamics.mdp to grompp using "-f". Also,
feed state.cpt to grompp using "-t".
where equilibration.mdp and dynamics.mdp contain different values of nsteps
and of nstxout, nstvout, nstfout, and nstenergy.
My question is, to do this sort of continuation (where I'm ONLY changing
nsteps, nstxout, nstvout, nstfout, and nstenergy), should I use
"continuation = yes"?
The manual gives this description of continuation:
"This option was formerly known as unconstrained_start.
no: apply constraints to the start configuration and reset shells
yes: do not apply constraints to the start configuration and do not reset
shells, useful for exact coninuation and reruns"
I do not think that my system has any constraints, since all the bonds in
all molecules are flexible, with force constants specified in the .itp
files. If this is the case, then should I use continuation = yes? Or,
since I do not have constraints in my system, will it perhaps not make a
difference whether continuation is yes or no? Do you have any
recommendations?
If not using constraints, the continuation keyword is irrelevant. The key is to
be sure there are truly no constraints, including any that use SHAKE or LINCS
(i.e. a solute) or SETTLE (water). The water models present in Gromacs should
all be rigid (i.e. constrained using SETTLE). But if you're sure there are no
constraints and that this representation is proper, then you can ignore the
"continuation" keyword. Saying you "think" there are no constraints means there
is uncertainty, which means you have some checking to do ;)
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
