On 13/04/2012 10:44 AM, Juliette N. wrote:
Hello all,
I am trying to exclude a nonbonded interactions on the polymer chains using
grompp -f old.mdp -c old_em.gro -p nrexcl_new.top -o new.tpr
and mdrun -rerun command. but when I issue the command above grompp
takes many hours to finish and at the end grompp crashes (Killed).
This even leads to some weired hardware problem which gibes failure of
node having some CPUs..I mean when I get grompp failure, I am not able
to connect to the node anymore and will have to restart the node!
grompp gives:
Generated 332520 of the 332520 1-4 parameter combinations
Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 101 bonded neighbours molecule type 'Polymer'
Can anyone help me please?
Justin explained the fundamental reason for the problem. Apparently the
implementation of the nrexcl=large is not robust with respect to memory
usage and/or CPU time for large numbers of exclusions. So you will have
to use energy group exclusions like I suggested earlier in this thread.
Mark
Thanks
On 8 April 2012 17:16, Justin A. Lemkul<jalem...@vt.edu> wrote:
Juliette N. wrote:
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.
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
========================================
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