Did you set the -f parameter to point to the right file? Never used
g_rotacf, but traj.xtc is the default file name for the trajectory
file.
// Linus
On Sun, Feb 17, 2013 at 12:57 PM, Sabrina Kemmerer
wrote:
> Hi,
>
> I copied the output files of my simulation on another computer and tried to
>
Both are probably using 4 cores, the first one as threads, the second via mpi.
However, in the second one you are using 16 threads to run 4 copies of
the same simulation, 4 threads each, thus getting performance similar
(or less) to using only one core. When using mpi, you should use
mdrun_mpi ins
If you install package 1 on your list, the second one will be
installed as well (ie you need both of them).
// Linus
On Mon, Jul 30, 2012 at 10:56 AM, rama david wrote:
> Hi GROMACS FRIENDS,
> I have dell T3500 precision, 64 bits, 6C workstation with fedora
> operating system.
> I want to
Quite sure it's just different syntax in topology and mdp file. Compare to C;
#define POSRES // expressed as -DPOSRES in the mdp file
#ifdef POSRES // when working in the topology file
// Linus
On Thu, Jul 26, 2012 at 1:52 PM,
wrote:
>>
>>
>> On 7/26/12 7:06 AM, reising...@rostlab.informatik.tu-
In order to use MPI on Ubuntu with the distribution-supplied package,
you need to use a combination of mpirun and mdrun_mpi, e.g.
mpirun -np 2 mdrun_mpi -deffnm md
to run on two cores.
On Mon, Dec 27, 2010 at 7:04 PM, Justin A. Lemkul wrote:
>
>
> גדעון לפידות wrote:
>>
>> Hi all,
>> I have rec
The nicelevel is simply the priority of the process, where 19 is the
lowest priority (ie most other programs will use the cpu before the
gromacs process does) and -20 the highest.
See man nice.
// Linus
On Tue, Dec 7, 2010 at 10:13 PM, GZ Zhang wrote:
> Hi, ALL
> I'm using "genbox" to crea
What did you try to do? To use dssp, you must select entire residues,
e.g. 1 (protein). That error sounds a bit like my problem when trying
to do dssp using only the backbone.
// Linus Östberg
On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# wrote:
> Hi,
>
> Thanks for your response, I modi
Use grompp normally, without the -np flag. Then run mdrun_mpi with your
normal parameters as mpirun -np x mdrun_mpi -deffnm xx
On Mon, Jun 21, 2010 at 2:00 PM, Amin Arabbagheri wrote:
> Hi all,
>
> I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic
> package manager.
> I want to
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