[gmx-users] The right way of killing Gromacs

Hello, the runtime of our cluster is unfortunately limited. Before mdrun is terminated a USR1 signal is send, but this doesn't cause mdrun to writeout the current frame. Therefore most of the trajectory is lost. I'd like to write a skrip which converts the USR1 sinal to some other signal. The q

Re: [gmx-users] Measuring dihedral energy of various selections

Thanks a lot! Sometimes it can be sooo easy ciao Jan Neumann >> may I ask how do you get the potential energies from a >> simulation? Is it possible to get continuous energy-time >> graph for a system? >> > > Use the script g_energy on the .edr file from the simulation. > > Catch ya, >

Re: [gmx-users] Measuring dihedral energy of various selections

Hi, may I ask how do you get the potential energies from a simulation? Is it possible to get continuous energy-time graph for a system? thanks in advance Jan Neumann David Mobley schrieb: > Maybe this is what someone is getting at in their answers, but you > COULD sort of "invert" the problem: U

Re: [gmx-users] empty energy file

Hi Mark, hi Dallas, I'll try your suggestion. Thanks a lot!! Jan Mark Abraham schrieb: > kobi wrote: >> Hello, >> >> I have got a little Problem here. Since I added the option "-t >> 2nd_equi.trr" to my grompp command to takeover all >> veloci

[gmx-users] empty energy file

Hello, I have got a little Problem here. Since I added the option "-t 2nd_equi.trr" to my grompp command to takeover all velocities from my equillibrated state, my energy file (full.edr) is created, but nothing is written to it any more. Could anybody tell me what I did wrong? My runs were abort

Re: [gmx-users] Gromacs-mpi with Rocks v4.0

Oh, thanks for correction. I'm sorry I got the exact details wrong. Didn't want to confuse anyone. Jan Mark Abraham schrieb: > kobi wrote: >> Hi Francisco >> >> If you intalled gromacs-mpi directly, then try to use just mdrun instead >> of mdrun_mpi. Norm

Re: [gmx-users] Gromacs-mpi with Rocks v4.0

Hi Francisco If you intalled gromacs-mpi directly, then try to use just mdrun instead of mdrun_mpi. Normally you only have a mdrun_mpi if the singleprocessorversion was installed first and you only added the multiprocessorversion afterwards. ciao Jan Francisco Tufró schrieb: > David, thanks for

Re: [gmx-users] AFM Pulling Rate

Hello Bob, have you tried to define the initial position of the AFM-tip? It needs to be set to the position of the COM of the group you want to pull. try and add "afm_init1 = x y z" (x y z = position where the afm should be) to your pull.ppa. Otherwise your afmspring is extended from the begin

[gmx-users] Parameters for OPLS

rature Coupling ist turne on (berendsen) and Pressure Coupling is turend off. The size of the box is 4x5.8x10 nm. thanks Kobi -- "Feel free" mit GMX FreeMail! Monat für Monat 10 FreeSMS inklusive! http://www.gmx.net ___ gmx-users