[gmx-users] gromacs Query
Aman Deep
r.amandeep2677 at gmail.com
Fri Apr 7 15:14:31 CEST 2017
thank you sir I have applied nstxout, nstvout, nstfout as zero and it is
now working
Thankyou
On Fri, Apr 7, 2017 at 6:04 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> 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
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--
Aman Deep
MSc Bioinformatics
Jamia Millia Islamia
New Delhi - 110025
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