Moeed wrote:
Dear GROMACS experts,
Initially I wanted to do MD for a stack of hexane molecules. MD showed
very high repulsion potential. On the recommendation of Justin, I
simplified the problem and now I have only one Hexane molecule.
1- I dont know why I do not get the written pdb files normally generated
after MD! I want to watch the trajectory.
What files are you talking about? The trajectory file is written in .trr format
(or optionally, .xtc format if you have nstxtcout > 1).
2- Could you please kindly take a look at energy values and let me know
if values are reasonable so that I can proceed to building stack of
hexane molecules. Pon
Your results are fine. You have a single hexane molecule in isolation so you
may not get a negative potential energy, which is a normal criterion for
stability.
3- Please help me understand NOTE 2 in output.grompp_md (end of this
post message)
<snip>
A lot of this information was unnecessary, and repetitive from your previous
posts.
Estimate for the relative computational load of the PME mesh part: 0.97
NOTE 2 [file aminoacids.dat, line 1]:
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for higher performance, increase the cut-off and the PME grid spacing
The error message is quite explicit, but is nothing you need to worry about.
Your system is not one that lends itself to optimization. A single molecule in
isolation does not parallelize very well (nor do you need it to). If you get
this message from a larger system, then you may have some inappropriate
settings, but for now, don't worry.
-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 gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
