Gromacs software Manual
Contents
1. ND2. 1 1369s 1 1382s 2 663s 2 06 4 351s 3 9 8 203s 6 74 202s 8 4 4 204s 6 71 205s 8 2 2 2 2 208s 6 58 16 8 8 143s 9 57 24 4 4 4 4 4 4 259s 5 29 32 8 8 8 8 109s 12 56 40 8 8 8 8 8 116s 11 8 48 8 8 8 8 8 8 111s 12 33 2 share gromacs tutor speptide Gromacs pdb 100ps full mdp nsteps CPU amp wallclock CPU 1 505s 1 2 244s 207 4 128s 3 95 8 70s Tel 8 4 4 70s 7 21 8 2 2 2 2 72s 7 01 3 1 share gromacs tutor mixed 2 o mpirun machinefile HOSTFILE np NPROCS home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 4 0 4 bin mdrun_d s topol v N 30 4 LB HOME bashre export PATH PATH home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 4 0 4 bin export GMXLIB home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 4 0 4 share gromacs t op bsub bsub W MIN n NPROCS a intelmpi q QUEUE e J
3. Gromacs upgrade to gromacs 4 0 7 2010 5 H FA ABE At ee 1 A een nee ne enges 2 E E nee 3 DS UA a re noch eed et a e 3 2 1 Ne 3 2 2 nn 3 A e ee 3 1 GROMACS FR GROMACS GROMACS MPI 3 3 3 2 2 1 home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 3 3 3 2 2 mnn n cpu m 1 share gromacs tutor mixed CPU amp wallclock CPU 1 1394s 2 899s 4 513s 8 343s 8 4 4 367s 8 2 2 2 2 371s 16 8 8 914s 24 4 4 4 4 4 4 1312s 3 1 share
4. err o J out mpirun lsf mdrun_d s INPUT v N 30 MIN NPROCS QUEUE s INPUT v N 30 4 0 3 2 1 home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 4 0 3 2 2 mon n cpu m p 1 share gromacs tutor mixed 1 1157s 1 2 550s 2 1 4 304s 3 8 8 176s 6 6 8 4 4 178s 6 5 8 2 2 2 2 183s 6 3 3 1 share gromacs tutor mixed 2 o mpirun machinefile HOSTFILE np NPROCS home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 4 0 3 bin mdrun s topol tpr v o md_traj 4 LB HOME bashre export PATH PATH home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 4 0 3 bin export GMXLIB home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 4 0 3 share gromacs t op bsub bsub W MIN n NPROCS a intelmpi q QUEUE e J err o J out mpirun lsf mdr
5. gromacs tutor water 2 bin grompp_d np NPROCS NPROCS 2 o mpirun machinefile HOSTFILE np NPROCS home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 3 3 3 bin mdrun_d s topol v N 30 4 LB HOME bashre export PATH PATH home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 3 3 3 bin export GMXLIB home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 3 3 3 share gromacs t op bsub bsub W MIN n NPROCS a intelmpi q QUEUE e J err o J out mpirun lsf mdrun_d s INPUT v N 30 MIN NPROCS QUEUE s INPUT v N 30 4 0 4 Ze 1 Un home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 4 0 4 2 2 mnn mn cpu Him 1 share gromacs tutor mixed CPU amp wallclock CPU
6. un s INPUT v o OUTPUT MIN NPROCS QUEUE s INPUT v o OUTPUT 4 0 7 2010 5 13 14 gromacs 4 0 7 disable float enable double home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 4 0 7 enable float AY home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 4 0 7 float source home soft soft x86 64 apps OpenSoft Chem gromacs gromacs 4 0 7 float bin GMXRC source home_soft soft x86_64 apps OpenSoft Chem gromacs gromacs 4 0 7 bin GMXRC 5 3 Gromacs 6 1 Gromacs3 3 3 4 0 4 4 0 3 15 2 16 cpu 60
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Gromacs software Manual