[gmx-users] Re: gmx-users Digest, Vol 92, Issue 30

[lloyd riggs]

> 
> Message: 2
> Date: Wed, 07 Dec 2011 00:12:19 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] RE: logfile size
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4EDE14B3.8040904 at anu.edu.au>
> 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 <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] RE: logfile size
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4EDE2DD3.50701 at anu.edu.au>
> 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.

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