On 2/04/2012 1:57 PM, Juliette N. wrote:
Hi all,
Is there anyway mdrun -rerun can be used on multiple nodes? e.g. -nt?
Yes. You could have just tried it :-) It's just a version of mdrun that
gets configurations from the magic file, doesn't actually do integration
steps and does neighbour searching every configuration.
Mark
Best,
---------- Forwarded message ----------
From: Juliette N.<joojoojo...@gmail.com>
Date: 1 April 2012 22:10
Subject: Re: [gmx-users] mdrun -rerun
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
On 1 April 2012 22:07, Mark Abraham<mark.abra...@anu.edu.au> wrote:
On 2/04/2012 12:05 PM, Juliette N. wrote:
Thanks. One last question. So whats the new trr file provided by -o
flag of mdrun rerun below?
mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e new
If it even writes one, it will be identical to the -rerun file. There's no
way for the rerun code to get new configurations except by reading the input
trajectory.
Thanks a lot :)
Mark
On 1 April 2012 20:17, Mark Abraham<mark.abra...@anu.edu.au> wrote:
On 2/04/2012 10:10 AM, Juliette N. wrote:
Hi all,
I have an enquiry regarding calculation of heat of vaporization by
estimating intermolecular nonbonded energies using mdrun rerun option.
mdrun
-rerun should break the total nonbonded energy coming from nonboded
energy
of (different molecules + a molecule with itself). By setting
appropriate
nrexcl in top file I am trying to exclude nonbonded part of molecule
with
itself within cut off radius so what remains would be intermolecular
nonbonded energy between different molecules which determines heat of
vaporization.
1) Is this approach correct?
For excluding a whole molecule, it could work. For excluding only a
part,
using energy group exclusions (see manual) is more flexible. Just
setting
energy groups suitably might work in your case, so that you get the
group-wise break-down of nonbonded energy.
Thank you Mark. I have a one component system. I guess group exclusions
is used for multicomponent systems where one needs to breakdown the
total
energies.? In my case I need to exclude non bonded interaction of a
polymer
chain with itself (avoid calculation of 1 and last atoms on chains if
they
fall within cutoff radius)
2) If yes, can you please check the way I am applying mdrun rerun:
grompp -p nrexcl_3.top -o total_nonbonded.tpr
mdrun -deffnm total_nonbonded -s -o -c -g -e
I am done with these 5ns runs and now intend to exclude nonbonded
interaction on a chain by increasing nrexcl in top file named
nrexcl_new.top
grompp -p nrexcl_new.top -o new.tpr
mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e
new
2) Am I doing this correctly? I doubt because I provide -rerun
total_nonbonded.trr but dont know how to introduce -rerun
total_nonbonded.edr so that new energies get written on it?
You want to write new energies and keep the old ones in case you need
them.
There's no reason to (want to) re-introduce the old ones. mdrun -rerun
accepts the trajectory to determine what configurations to compute
about.
It
doesn't need to know what some other algorithm thought about the
energies
of
that configuration.
I am a bit puzzled now. mdrun run takes on the old trajectory and
recomputes energies based on the old trajectory for each frame?
Yes, per mdrun -h.
If thats the case, then use of nrexcel in order to obtain new
trajectories fails I guess, as mdrun rerun does not produce a new
trajectory
but only a new energy file?!
In other words, say I am doing NPT, with default nrexcel =3 I got a
trajectory file and a density. Now with a new nrexcel that is large
enough to exclude all nonbonded interactions of atoms on the same
chain, I should expect a new trajectory and new density corresponding
to this modified nrexcel. My concern is if what mdrun reruns does is
just computing energies based on the old trajectory, I need to redo
the simulations with a new top file (nrexcel=new number) because this
new top file should affect the configuration. Am I right?
If you want new configurations based on some Frankenstein of your model
physics, then you do not need mdrun -rerun.
Mark
So for instance,
3) If I want to re-calculate only the last 1 ns of runs (after system
is
equilibrated), can I use -b 4000 ? i.e.:
mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e
new
-b
4000
Probably not. Check mdrun -h, but either way you can use trjconv first.
Mark
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Thanks,
J. N.
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