Please keep all Gromacs-related correspondence on the gmx-users list. This has
nothing to do with any of my tutorials, and as such, is better posted to the
community. As I seem to post every other day or so, I am not a private tutor or
help service.
The grompp.mdp file in the /share/tutor subdirectory is outdated. A quick look
at the manual explains warning #1; this parameter does not exist. The other two
notes are clearly explained by grompp. For the purposes of running through the
example in /share/tutor, you can set -maxwarn 1 (which is not generally
advisable, but in this case is OK), or modify the grompp.mdp file to contain
relevant settings.
-Justin
mohammad Kowsari wrote:
Dear Justin,
I mailed to you in the previous month about your gromacs tutorials.
now, I start with gromacs tutor sub-directory in the share folder.
for example, for both water and methanol example, when I run grompp -v
, I see these problem message:
WARNING 1 [file grompp.mdp, line unknown]:
Unknown or double left-hand 'bd-temp' in parameter file
NOTE 1 [file grompp.mdp, line unknown]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
NOTE 2 [file grompp.mdp, line unknown]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
Program grompp, VERSION 4.0.5
Source code file: gmx_fatal.c, line: 481
Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
-------------------------------------------------------
in these condition, gromacs generate "mdout.mdp" file but no generate
"topol.tpr" file.
when I used this options: grompp -v -maxwarn 1
the pre-processing is done and the topol.tpr file is constracted.
Is it possible and correct to use of "-maxwarn 1" for run these
tutorial example or not?!?
Best Regards,
M. H. Kowsari
PhD of Physical Chemistry
Isfahan University of Technology, 84156-83111
Isfahan, IRAN
--
========================================
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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