[gmx-users] gromacs Query

Fri Apr 7 14:34:53 CEST 2017

Hi,

On Fri, 7 Apr 2017 11:18 Aman Deep <r.amandeep2677 at gmail.com> wrote:

> sir, I didn't understand what is E here ???
>

As Justin suggested, that was a typo for "maybe".

and after removing  nstxout  still, it is not helping..
>

I did not suggest doing that. I did ask what your GROMACS version was.

Don't use both nstxtcout and nstxout-compressed (which is its successor,
but maybe not understood by old versions of GROMACS, but I can't help you
if you won't share that information :-)).

Mark

On Fri, Apr 7, 2017 at 1:25 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > Which version of GROMACS is this? The only problem I can see is that you
> > are using both nstxtcout and its successor (don't), and may E that is
> > confusing the parser.
> >
> > Mark
> >
> > On Fri, 7 Apr 2017 07:41 Aman Deep <r.amandeep2677 at gmail.com> wrote:
> >
> > > sir, i am using this output control but still, it is generating same
> > space
> > > data
> > >
> > >
> > > ; Run parameters
> > > integrator = md            ; leap-frog integrator
> > > nsteps          = 25000000 ; 2 * 500000 = 50000 ps (50 ns)
> > > dt                  = 0.002             ; 2 fs
> > >
> > > ; Output control
> > > nstxout         = 0             ; save coordinates every 10.0 ps
> > > nstxtcout               =2500000                ; save velocities every
> > > 50.0 ps
> > > nstenergy               = 2500000               ; save energies every
> > 50.0
> > > ps
> > > nstlog                  = 2500000 ; update log file every 50.0 ps
> > > nstxout-compressed = 2500000      ; save compressed coordinates every
> > 10.0
> > > ps                                ; nstxout-compressed replaces
> nstxtcout
> > > xtc-grps                = Protein     ; replaces xtc-grps
> > >
> > >
> > > On Mon, Apr 3, 2017 at 3:15 PM, Mark Abraham <mark.j.abraham at gmail.com
> >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > If you ask for .trr output, you get it. Stop using non-zero nst*out
> mdp
> > > > settings that you don't want.
> > > >
> > > > Mark
> > > >
> > > > On Mon, Apr 3, 2017 at 11:31 AM Aman Deep <r.amandeep2677 at gmail.com>
> > > > wrote:
> > > >
> > > > > sir,
> > > > >
> > > > > I have tried *nstxctout  *but it still making trr file ... is there
> > any
> > > > > option to  make only xtc file ???
> > > > >
> > > > > On Mon, Apr 3, 2017 at 1:14 PM, Mark Abraham <
> > mark.j.abraham at gmail.com
> > > >
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > See
> > > > > >
> > > > > http://www.gromacs.org/Documentation/How-tos/
> > > > Reducing_Trajectory_Storage_
> > > > > > Volume
> > > > > >
> > > > > > Mark
> > > > > >
> > > > > > On Mon, Apr 3, 2017 at 9:27 AM Aman Deep <
> r.amandeep2677 at gmail.com
> > >
> > > > > wrote:
> > > > > >
> > > > > > > sir is there any way to create only XTC file from mdrun only.
> the
> > > > > server
> > > > > > on
> > > > > > > which I am working is not providing enough space and my trr
> file
> > is
> > > > too
> > > > > > > much large.
> > > > > > >
> > > > > > > thank you
> > > > > > >
> > > > > > > --
> > > > > > > Aman Deep
> > > > > > > MSc Bioinformatics
> > > > > > > Jamia Millia Islamia
> > > > > > > New Delhi - 110025
> > > > > > > --
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> > > > > --
> > > > > Aman Deep
> > > > > MSc Bioinformatics
> > > > > Jamia Millia Islamia
> > > > > New Delhi - 110025
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> > > --
> > > Aman Deep
> > > MSc Bioinformatics
> > > Jamia Millia Islamia
> > > New Delhi - 110025
> > > --
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>
> --
> Aman Deep
> MSc Bioinformatics
> Jamia Millia Islamia
> New Delhi - 110025
> --
> Gromacs Users mailing list
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