> > Message: 2 > Date: Wed, 07 Dec 2011 00:12:19 +1100 > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] RE: logfile size > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > On 6/12/2011 8:48 PM, lloyd riggs wrote: > > Dear All, > > > > Hope this is not tooo stupid a question. I recenttly reduced my file > sizes by increasing the time between writing. However, if I do an Umbrella > run I get the following to my logfile output, which makes my log file in the > end larger than my trajectory; > > > > .... > > Dispersion correction V -5.49759e+03 dVdl 0.00000e+00 > > Dispersion correction V -5.49756e+03 dVdl 0.00000e+00 > > Dispersion correction V -5.49753e+03 dVdl 0.00000e+00 > > Dispersion correction V -5.49750e+03 dVdl 0.00000e+00 > > Dispersion correction V -5.49747e+03 dVdl 0.00000e+00 > > Dispersion correction V -5.49744e+03 dVdl 0.00000e+00 > > Dispersion correction V -5.49741e+03 dVdl 0.00000e+00 > > Dispersion correction V -5.49738e+03 dVdl 0.00000e+00 > > Dispersion correction V -5.49735e+03 dVdl 0.00000e+00... > > > > Does anyone know how to turn this off for the logfile, I get one of > these for each step, instead of for each write step? My write portion of the > .mdp file is; > > > > nsteps = 20000000 ; 2 * 50000 = 100 ps > > dt = 0.0002 ; 2 fs > > tinit = 0 > > ; Output control > > nstxout = 100000 ; save coordinates every 0.2 ps > > nstvout = 100000 ; save velocities every 0.2 ps > > nstenergy = 100000 ; save energies every 0.2 ps > > nstcalcenergy = 100 > > nstfout = 100000 > > nstlog = 100000 ; update log file every 0.2 ps > > nstxtcout = 100000 > > > > Check out the list of options in mdrun -h. There's one that will > completely stop this printing. > > I think it's supposed to print this stuff only according to nstlog, but > the code is slightly broken here. I'll suggest a fix. > > Mark > > > ------------------------------ > > Message: 3 > Date: Wed, 07 Dec 2011 01:59:31 +1100 > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] RE: logfile size > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > On 7/12/2011 12:12 AM, Mark Abraham wrote: > > On 6/12/2011 8:48 PM, lloyd riggs wrote: > >> Dear All, > >> > >> Hope this is not tooo stupid a question. I recenttly reduced my file > >> sizes by increasing the time between writing. However, if I do an > >> Umbrella run I get the following to my logfile output, which makes my > >> log file in the end larger than my trajectory; > >> > >> .... > >> Dispersion correction V -5.49759e+03 dVdl 0.00000e+00 > >> Dispersion correction V -5.49756e+03 dVdl 0.00000e+00 > >> Dispersion correction V -5.49753e+03 dVdl 0.00000e+00 > >> Dispersion correction V -5.49750e+03 dVdl 0.00000e+00 > >> Dispersion correction V -5.49747e+03 dVdl 0.00000e+00 > >> Dispersion correction V -5.49744e+03 dVdl 0.00000e+00 > >> Dispersion correction V -5.49741e+03 dVdl 0.00000e+00 > >> Dispersion correction V -5.49738e+03 dVdl 0.00000e+00 > >> Dispersion correction V -5.49735e+03 dVdl 0.00000e+00... > >> > >> Does anyone know how to turn this off for the logfile, I get one of > >> these for each step, instead of for each write step? My write > >> portion of the .mdp file is; > >> > >> nsteps = 20000000 ; 2 * 50000 = 100 ps > >> dt = 0.0002 ; 2 fs > >> tinit = 0 > >> ; Output control > >> nstxout = 100000 ; save coordinates every 0.2 ps > >> nstvout = 100000 ; save velocities every 0.2 ps > >> nstenergy = 100000 ; save energies every 0.2 ps > >> nstcalcenergy = 100 > >> nstfout = 100000 > >> nstlog = 100000 ; update log file every 0.2 ps > >> nstxtcout = 100000 > >> > > > > Check out the list of options in mdrun -h. There's one that will > > completely stop this printing. > > > > I think it's supposed to print this stuff only according to nstlog, > > but the code is slightly broken here. I'll suggest a fix. > > Nah, the code looks fine - it should only ever print at nstlog steps. > > Mark > >
Dear Mark, I just compacted it, but I had never done that in the past and never had that? It only came up as of late. Stephan Watkins > Check out the list of options in mdrun -h. There's one that will > completely stop this printing. -- NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! Jetzt informieren: http://www.gmx.net/de/go/freephone -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
