Hi Albert,
Please accept my apologies, I must have misread your e-mail. Effectively
everything seems to be right in the command line and I am not able to
understand either why you get the error.
Good luck.
Cheers,
Davide
On 19/10/12 7:54 PM, "Albert" wrote:
>hello David:
>
>thanks for kind r
When calculated during the md run, the corresponding options in g_energy
for the dipole moment are MU-X, MU-Y and MU-Z.
However, taking into account the previous mail by David van der Spoel,
it's possible that the dipole moment could not be calculated in your
system. Options in g_energy vary d
Dear Gromacs,
I am trying to install gromacs with mpi enabled in my cluster and i end
up with following error:
libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled
argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error
I can able to install gromacs i
Dear Rajiv,
Please start a different thread, if you want to get help. I suppose
you need to be informative regarding your error(s).
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Oct 19, 2012 at 2:07 PM, Rajiv Gandhi wrote:
> Dear Gromacs,
>
> I am trying to install gromacs with m
On 10/19/12 2:37 AM, Albert wrote:
hello:
I am trying to submit replica exchange jobs to cluster by following command, but
failed:
g_tune_pme_d -x -np 128 mdrun -s remd_.tpr -multi 16 -replex 1000 -reseed -1
-launch
Here is the log file:
-
Dear all,
A simple question.
I want to change the md command line in a script. I want to prevent my
script to lead the simulation on parallel nodes. By this I mean I want to
run it on one CPU. I do not know where I should embed the flag -nt=1 in that
command lien.
I wonder the following is the md
Dear Gromacs,
I am trying to install gromacs with mpi enabled in my cluster and i end
up with following error:
libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled
argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error
I can able to install gromacs i
On 10/19/12 7:16 AM, Arman M. Soufiani wrote:
Dear all,
A simple question.
I want to change the md command line in a script. I want to prevent my
script to lead the simulation on parallel nodes. By this I mean I want to
run it on one CPU. I do not know where I should embed the flag -nt=1 in th
Sorry, Ali, it's not really possible for me to simplify those commands. That's
about as simple as it gets.
I suggest that you start a normal post that follows the form: I did this (paste
commands) and I got this
(paste error message). Also, when you get a message like
Fatal error:
Invalid lin
Dear Ali:
Please also keep in mind that 99% of the papers published with gromacs using
NpT have shown density profiles
along Z that were computed simply by using (the incorrect) trjconv -center and
(the incorrect for NpT) g_density.
So while I think that it's always important to get things righ
Dear Vitaly,
I appreciate your informative response.
Dear Justin,
Thank you for your kind helps.
On Fri, Oct 19, 2012 at 5:31 PM, Dr. Vitaly Chaban wrote:
> > Dear all,
> >
> > A simple question.
> > I want to change the md command line in a script. I want to prevent my
> > script to lead the
Hi,
When it comes to hardware, pretty much the only thing that matters is
processors (CPUs and maybe GPUs) , memory will always be more than enough
-- unless you plan to run massive analysis in the cloud. In general, if
your simulation system runs fast enough on a single compute node (1-2
CPUs), t
My point is that the old paper probably used the incorrect trjconv/g_density as
well so to "reproduce" it you may
be best off using the standard gromacs.
Chris.
-- original message --
Thank you so much for your reply but it is very important for me that
i can reproduce
results of a paper or no
Sorry Ali, I can't do your work for you. If this is way over your head, then
either forget it, find a colleague to help
you, or spend some time learning bash and gromacs. I'n not commenting on your
approach, but if you modified
your .gro then you need a new .top file. You can create one.
Chris.
At Rescale (www.rescale.com) we have cloud-based options for 10Gb/s
I/O to run mpi versions of Gromacs. The performance for these has
been very good and can scale to hundreds of simulation dynos
(computing nodes).
Regardless of which service you use, I would highly recommend trying
some of the cl
The solution that I have posted with modified trjconv -center gives the correct
values. However, you should always
check such things because at the end of the day it is your name on the paper so
you are the one responsible.
If you want to reproduce a previous result, just contact them to find ou
16 matches
Mail list logo