chris.ne...@utoronto.ca wrote:
You'll need to provide a much better report than this if you want to
receive any useful help.
Copy and paste the exact commands of what you did
Copy and paste the exact log file and error messages
I'd also add that we need a detailed description of the system, including force
field used and any other special considerations (distance restraints, modified
parameters, etc). An .mdp file would also be useful for the run that crashes.
-Justin
Do this for 4.0.7 and 4.5.4, for which I trust that you have been using
exactly identical test systems. If not, then please try it again while
conserving the system.
Chris.
-- original message --
Hi Matthew,
Thanks for the reply. First, I don't thinks it is poorly compiled bin, as I
used both GROMACS compiled by me (on my machine) or by the sys-admin on
Linux cluster or blue-gene.
The simulations using 4.5.4 crashed giving LINCS error, which is not the
case with 4.0.7 (using the same mdp and pdb files). Second, I don't thinks
it is poorly compiled bin, as I used both GROMACS compiled with me (on my
machine) or by the sys-admin on Linux cluster/blue-gene.
cheers,
Itamar
On 18 August 2011 01:48, Matthew Zwier <mczwier at gmail.com> wrote:
Could be a system blowing up, or perhaps a mis-compiled binary. What
error messages do you get when the crash occurs?
On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass <itamar.kass at monash.edu>
wrote:
> Hi all GROMACS useres and developers,
>
> I am interesting in simulating a small protein (~140 aa) in water, with
and without Ca ions. In order to do so, I had used version 4.5.4. I had
solvate the protein in water, add ions to naturalise the systems,
equilibrated the systems and then tried productive runs. Now, no
matter what
I did, it crashed after few ps's of free MD or during the PR runs.
>
> Few of the things I had tried are:
> 1. Running the simulations on different systems (OSX, linux or
blue-gene).
> 2. Using single or double precision versions.
> 3. An equilibration stage, 1ns long with a time-step of 1fs, during
which
the restrained forces where gradually reduced from 1000 to 50 kJ mol-1
nm-2.
> 4. Running part of the equilibration stage as NVT and then switched to
NPT.
> 5. Started from different x-ray structures, with resolutions differ
from
2.5 to 1.7 Angstrom.
>
> Finally I had moved back to 4.0.7 which worked like charm. I wonder if
someone else had encounter something like this. Attached please find
the mdp
files I used.
>
> All the best,
> Itamar.
>
>
>
>
--
========================================
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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