You'll want to look up redirection operators for whatever shell
you're using, but here are a couple suggestions:
grompp (usual args) >& file.dat
- or -
grompp (usual args) 2> file.dat
--Tom
On Jun 1, 2006, at 2:36 PM, David Mobley wrote:
So, this is probably a stupid question, but for som
Can you try to generate a backtrace for the mknb crash using gdb, in case this offers some insight?$ gdb mknbgdb> r -software_invsqrt...gdb> bt(backtrace output appears here)--TomOn May 31, 2006, at 11:33 AM, Jones de Andrade wrote:Hi David. First, thanks for your time. ;) Unfortunatelly, it seem
You need to install the gcc-g77, openssh-clients, and openssh-server packages, and any packages they may depend on. This isn't a GROMACS question - please read the documentation from OpenSuse regarding installing new packages.--TomOn May 8, 2006, at 2:24 PM, Jayant James Jayasundar wrote: hi ! I a
It is in fact possible. You can tell LAM (or probably any other self-
respecting MPI package) to make use of 4 CPUs on one node; see the
documentation for lamboot and its hosts file.
--Tom
On Apr 25, 2006, at 10:55 AM, <[EMAIL PROTECTED]>
<[EMAIL PROTECTED]> wrote:
hello,
i would like
This is probably the result of a bug in 3.3, fixed in 3.3.1. Setting
pme_order = 4 is a workaround in case you don't want to upgrade to
3.3.1.
--Tom
On Apr 19, 2006, at 11:05 AM, Zorzan Simone wrote:
Hi all, I am trying to do the Drug Enzyme tutorial
(trp_drug_tutor.pdf),
on a linux box
Providing a backtrace or two would really help. Given the exact same input files and run conditions, does it sometimes segfault and sometimes not? Does this happen on a login node (full glibc and such) or just the compute nodes (POSIX subset)?Separately, is it a better idea to use fftw2 since it s
One possibility is Modloop:
http://alto.compbio.ucsf.edu/modloop/modloop.html
...which is a function of MODELLER:
http://salilab.org/modeller/
--Tom
On Apr 6, 2006, at 2:25 PM, Jayant James Jayasundar wrote:
Hi friends!
Part of a molecule that I am trying to simulate is not
crystallograph
The authors of the following paper implemented Generalized Born in
GROMACS. They seem willing to send their modifications to people who
email them and ask.
Comparative study of generalized Born models: protein dynamics. Proc
Natl Acad Sci U S A. 2005 May 10;102(19):6760-4. Epub 2005 Apr 6
A wild guess: SGI's compiler doesn't support some language feature or
other in the same way as expected by the GROMACS source code. So, if
you have gcc installed, you might try compiling using that.
setenv CC `which gcc`
./configure --put-your-parameters-here
--Tom
On Apr 3, 2006, at 8:32
In your em.mdp file, make sure that the "cpp" variable is set to the
location of your C preprocessor binary. To find out where it is,
type "which cpp" at the command line.
--Tom
On Apr 2, 2006, at 1:18 PM, Kushal Seth wrote:
hi all !
I am trying to run the following command -
grompp -np 2
ing problems due to *known bugs* in 3.3 simply because
there
is no easy way to find out about these bugs or their solutions.
David
On 3/29/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
Tom Joseph wrote:
Curiously, what is pme_order set to in your mdp file? I
experienced a
very
t a bit nervous that people
may be having problems due to *known bugs* in 3.3 simply because there
is no easy way to find out about these bugs or their solutions.
David
On 3/29/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
Tom Joseph wrote:
Curiously, what is pme_order set to in your m
Curiously, what is pme_order set to in your mdp file? I experienced a
very similar problem as you did when I had set pme_order to 6, and I
don't know why...
--Tom
On Mar 28, 2006, at 10:28 PM, raja wrote:
Hi gmxs,
No reply yet for this posting, so I reposting the same
error...P
Certainly you should consult your documentation, but one possibility is:
mpirun -np 8 mdrun_mpi -np 8 -s pr -o pr -c after_pr -e pr -g pr -v -
N 8
--Tom
On Mar 21, 2006, at 6:48 PM, Erik Lindahl wrote:
mdrun_mpi -np 8 mdrun -np 8 -s pr -o pr -c after_pr -e pr -g pr -
v -N 8
This won't
14 matches
Mail list logo
