[gmx-users] 3 questions of gromacs 4.5.2 for both CPU and GPU

Hi, I am testing the dhfr benchmarks with gromacs 4.5.2 1. for the benchmarks: dhfr-solv-RF-1nm.bench and dhfr-solv-RF-2nm.bench, set the steps = 1, The GPU version running results shows as following: ./mdrun-gpu Pre-simulation ~15s memtest in progress...done, no errors d

[gmx-users] 3 questions of gromacs 4.5.2 for both CPU and GPU

hi, I am testing the dhfr benchmarks with gromacs 4.5.2 1. for the benchmarks: dhfr-solv-RF-1nm.bench and dhfr-solv-RF-2nm.bench, set the steps = 1, The GPU version running results shows as following: ./mdrun-gpu Pre-simulation ~15s memtest in progress...done, no errors dete

RE: [gmx-users] ./mdrun

yeah，Thanks a lot :) YY > Date: Thu, 11 Nov 2010 20:32:55 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] ./mdrun > > > > lin hen wrote: > > It doesn't work, even I deleted this line > > it stills sho

RE: [gmx-users] ./mdrun

It doesn't work, even I deleted this line it stills shows the same error... I use ./mdrun-gpu without any flags. Did I miss something? YY > Date: Thu, 11 Nov 2010 20:25:45 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] ./mdrun &

RE: [gmx-users] ./mdrun

rol...@utk.edu Date: Tue, 9 Nov 2010 21:34:34 -0500 Subject: Re: [gmx-users] ./mdrun To: gmx-users@gromacs.org Hi, as you output says. It infinite long trajectory. Either set a number of steps (in mdp file or with tpbconf) or set a maximum time with (mdrun -maxh) Roland On Tue, Nov 9, 2010

[gmx-users] ./mdrun

Hi, I am using the dhfr gpu benchmark with mdrun-gpu:dhfr-solv-RF-2nm.bench. export LD_LIBRARY_PATH=/path to OPENMM lib and cuda lib/ export OPENMM_PLUGIN=/path to OPENMM lib plugins/ it shows: Back Off! I just backed up md.log to ./#md.log.1# Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b

RE: [gmx-users] ./mdrun-gpu fatal error

u > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] ./mdrun-gpu fatal error > > > > lin hen wrote: > > Thanks a lot for your reply, I didn't have this .mdp file, and I > > attached the log file, how to modify? > > > > You don't have an .

[gmx-users] ./mdrun-gpu fatal error

Hi, I am new for gromacs, I am trying to run the mdrun-gpu executable: the step to build the mdrun-gpu: 1. disable the shared libraries: //disable shared libraries (can be problematic with MPI, Windows) BUILD_SHARED_LIBS:BOOL=OFF 2. export LD_LIBRARY_PATH=/path to openmm2.0-Linux64/li