Re: [gmx-users] Can not open file: traj.xtc

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 >

Re: [gmx-users] Re: question about minimisation

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-

Re: [gmx-users] Gromacs installation

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

Re: [gmx-users] About system requirement to gromacs

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

Re: [gmx-users] dssp

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

Re: [gmx-users] what is the "nicelevel" ?

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

Re: [gmx-users] MPIRUN on Ubontu

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

Re: [gmx-users] (no subject)

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