Juliette N. wrote:
On 1 April 2012 20:17, Mark Abraham <[email protected]> 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.
2) If yes, can you please check the way I am applying mdrun rerun:
grompp -p nrexcl_3.top -o total_nonbonded.tpr
Hello all,
I am a bit confused about whether or not mdp file has to be provided
for grompp rerun step. In the original run (no mdrun I provide mdp as
follows:
grompp -f old.mdp -c old_em.gro -p nrexcl_3.top -o
total_nonbonded.tpr (GROMPP old)
then :
mdrun -deffnm total_nonbonded -s -o -c -g -e
Then I update the top file to new nrexcl= new value
No do I have to provide the old mdp file and old gro file old_em.gro,
which were used in (GROMPP old)? that is:
(GROMPP new:) grompp -f old.mdp -c old_em.gro -p nrexcl_new.top
-o new.tpr
mpirun –np 4 mdrun_mpi -rerun total_nonbonded.trr –deffnm new -s -o
-c -g -e -x
or I just have to use:
grompp -p nrexcl_new.top -o new.tpr ( no -c and no -f flag)
You need to provide some .mdp file and configuration. If you omit -c and -f,
grompp (like any other Gromacs program) will search for the default names of
grompp.mdp and conf.gro. If they don't exist, grompp will fail.
My other question is that the grompp with large nrexcl around 100 is
taking a lot of time, while the default nrexcl=3 was grompp ed much
faster. Why excluding bonds in this way is time consuming?
It's going slower because it's doing exponentially more work.
-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
========================================
--
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
