subject:"\[gmx\-users\] gromacs Query"

Re: [gmx-users] gromacs Query

2017-04-07 Thread Aman Deep

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 
wrote:

> Hi,
>
> On Fri, 7 Apr 2017 11:18 Aman Deep  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 
> > 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  wrote:
> > >
> > > > sir, i am using this output control but still, it is generating same
> > > space
> > > > data
> > > >
> > > >
> > > > ; Run parameters
> > > > integrator = md; leap-frog integrator
> > > > nsteps  = 2500 ; 2 * 50 = 5 ps (50 ns)
> > > > dt  = 0.002 ; 2 fs
> > > >
> > > > ; Output control
> > > > nstxout = 0 ; save coordinates every 10.0 ps
> > > > nstxtcout   =250; save velocities
> every
> > > > 50.0 ps
> > > > nstenergy   = 250   ; save energies every
> > > 50.0
> > > > ps
> > > > nstlog  = 250 ; update log file every 50.0 ps
> > > > nstxout-compressed = 250  ; 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.abra...@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.amandeep2...@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.abra...@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.amandeep2...@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
> > > > > > > > --
> > > > > > > > Gromacs Users mailing list
> > > > > > > >
> > > > > > > > * Please search the archive at
> > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > > before
> > > > > > > > posting!
> > > > > > > >
> > > > > > > > * Can't post? Read
> > http://www.gromacs.org/Support/Mailing_Lists
> > > > > > > >
> > > > > > > > * For (un)subscribe requests visit
> > > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> > > gmx-users
> > > > > or
> > > > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > > > >
> > > > > > > --
> > > > > > > Gromacs Users mailing list
> > > > > > >
> > > > > > > * Please search the archive at http://www.gromacs.org/
> > > > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > > > >
> > > > > > > * Can't post? Read http://www.gromacs.org/
> Support/Mailing_Lists
> > > > > > >
> > > > > > > * For (un)subscribe requests visit
> > > > > > >
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > > or
> > > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Aman Deep
> > > > > > MSc Bioinformatics
> > > > > > Jamia Millia Islamia
> > > > > > New Delhi - 110025
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the

Re: [gmx-users] gromacs Query

2017-04-07 Thread Mark Abraham

Hi,

On Fri, 7 Apr 2017 11:18 Aman Deep  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 
> 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  wrote:
> >
> > > sir, i am using this output control but still, it is generating same
> > space
> > > data
> > >
> > >
> > > ; Run parameters
> > > integrator = md; leap-frog integrator
> > > nsteps  = 2500 ; 2 * 50 = 5 ps (50 ns)
> > > dt  = 0.002 ; 2 fs
> > >
> > > ; Output control
> > > nstxout = 0 ; save coordinates every 10.0 ps
> > > nstxtcout   =250; save velocities every
> > > 50.0 ps
> > > nstenergy   = 250   ; save energies every
> > 50.0
> > > ps
> > > nstlog  = 250 ; update log file every 50.0 ps
> > > nstxout-compressed = 250  ; 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  >
> > > 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 
> > > > 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.abra...@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.amandeep2...@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
> > > > > > > --
> > > > > > > Gromacs Users mailing list
> > > > > > >
> > > > > > > * Please search the archive at
> > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > before
> > > > > > > posting!
> > > > > > >
> > > > > > > * Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
> > > > > > >
> > > > > > > * For (un)subscribe requests visit
> > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> > gmx-users
> > > > or
> > > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > > >
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the archive at http://www.gromacs.org/
> > > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > > >
> > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or
> > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Aman Deep
> > > > > MSc Bioinformatics
> > > > > Jamia Millia Islamia
> > > > > New Delhi - 110025
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at

Re: [gmx-users] gromacs Query

2017-04-07 Thread Justin Lemkul




On 4/7/17 6:17 AM, Aman Deep wrote:

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



I think Mark made a typo in writing the word "maybe" here.

The point he was making is that you're trying to specify nstxtcout and 
nstxout-compressed, which is a mixture of syntax from different GROMACS 
versions.  You can't/shouldn't do that.



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



All of the .trr options (nstxout, nstvout, nstfout) default to zero, so a .trr 
file is only written if you ask for it by setting any one of those to a non-zero 
value.


-Justin


On Fri, Apr 7, 2017 at 1:25 PM, Mark Abraham 
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  wrote:


sir, i am using this output control but still, it is generating same

space

data


; Run parameters
integrator = md; leap-frog integrator
nsteps  = 2500 ; 2 * 50 = 5 ps (50 ns)
dt  = 0.002 ; 2 fs

; Output control
nstxout = 0 ; save coordinates every 10.0 ps
nstxtcout   =250; save velocities every
50.0 ps
nstenergy   = 250   ; save energies every

50.0

ps
nstlog  = 250 ; update log file every 50.0 ps
nstxout-compressed = 250  ; 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 
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 
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.abra...@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

Re: [gmx-users] gromacs Query

2017-04-07 Thread Aman Deep

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

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

On Fri, Apr 7, 2017 at 1:25 PM, Mark Abraham 
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  wrote:
>
> > sir, i am using this output control but still, it is generating same
> space
> > data
> >
> >
> > ; Run parameters
> > integrator = md; leap-frog integrator
> > nsteps  = 2500 ; 2 * 50 = 5 ps (50 ns)
> > dt  = 0.002 ; 2 fs
> >
> > ; Output control
> > nstxout = 0 ; save coordinates every 10.0 ps
> > nstxtcout   =250; save velocities every
> > 50.0 ps
> > nstenergy   = 250   ; save energies every
> 50.0
> > ps
> > nstlog  = 250 ; update log file every 50.0 ps
> > nstxout-compressed = 250  ; 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 
> > 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 
> > > 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.abra...@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  >
> > > > 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
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the archive at
> > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before
> > > > > > posting!
> > > > > >
> > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> gmx-users
> > > or
> > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > >
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at http://www.gromacs.org/
> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Aman Deep
> > > > MSc Bioinformatics
> > > > Jamia Millia Islamia
> > > > New Delhi - 110025
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > Aman Deep
> > MSc Bioinformatics
> > Jamia Millia Islamia
> > New Delhi - 110025
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> >

Re: [gmx-users] gromacs Query

2017-04-07 Thread Mark Abraham

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  wrote:

> sir, i am using this output control but still, it is generating same space
> data
>
>
> ; Run parameters
> integrator = md; leap-frog integrator
> nsteps  = 2500 ; 2 * 50 = 5 ps (50 ns)
> dt  = 0.002 ; 2 fs
>
> ; Output control
> nstxout = 0 ; save coordinates every 10.0 ps
> nstxtcout   =250; save velocities every
> 50.0 ps
> nstenergy   = 250   ; save energies every 50.0
> ps
> nstlog  = 250 ; update log file every 50.0 ps
> nstxout-compressed = 250  ; 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 
> 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 
> > 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  >
> > > 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 
> > > 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
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > Aman Deep
> > > MSc Bioinformatics
> > > Jamia Millia Islamia
> > > New Delhi - 110025
> > > --
> > > Gromacs Users mailing list
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>
>
>
> --
> Aman Deep
> MSc Bioinformatics
> Jamia Millia Islamia
> New Delhi - 110025
> --
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Re: [gmx-users] gromacs Query

2017-04-07 Thread Aman Deep

sir, i am using this output control but still, it is generating same space
data


; Run parameters
integrator = md; leap-frog integrator
nsteps  = 2500 ; 2 * 50 = 5 ps (50 ns)
dt  = 0.002 ; 2 fs

; Output control
nstxout = 0 ; save coordinates every 10.0 ps
nstxtcout   =250; save velocities every
50.0 ps
nstenergy   = 250   ; save energies every 50.0
ps
nstlog  = 250 ; update log file every 50.0 ps
nstxout-compressed = 250  ; 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 
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 
> 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 
> > 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 
> > 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
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
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> > > Support/Mailing_Lists/GMX-Users_List before posting!
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > Aman Deep
> > MSc Bioinformatics
> > Jamia Millia Islamia
> > New Delhi - 110025
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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>



-- 
Aman Deep
MSc Bioinformatics
Jamia Millia Islamia
New Delhi - 110025
-- 
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Re: [gmx-users] gromacs Query

2017-04-03 Thread Mark Abraham

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  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 
> 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 
> 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
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Aman Deep
> MSc Bioinformatics
> Jamia Millia Islamia
> New Delhi - 110025
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] gromacs Query

2017-04-03 Thread Aman Deep

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 
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  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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Aman Deep
MSc Bioinformatics
Jamia Millia Islamia
New Delhi - 110025
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] gromacs Query

2017-04-03 Thread Mark Abraham

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  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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] gromacs Query

2017-04-03 Thread Aman Deep

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
-- 
Gromacs Users mailing list

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Re: [gmx-users] gromacs Query

Re: [gmx-users] gromacs Query

Re: [gmx-users] gromacs Query

Re: [gmx-users] gromacs Query

Re: [gmx-users] gromacs Query

Re: [gmx-users] gromacs Query

Re: [gmx-users] gromacs Query

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[gmx-users] gromacs Query

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