[gmx-users] regarding changing the scale from ps to ns

[Dallas Warren]

What didn't work? Highly recommend with things like this that you copy and
paste the exact command you tried and what the output was. Vague references
to it not working is not helpful to those looking to give advice on what to
do.

The suggested command by Reza was something like:

gmx trjconv -f input_pstime.xtc -o output_nstime.xtc -tu ns

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Thu, 29 Aug 2019 at 19:34, sudha bhagwati <sudhabhagwati at gmail.com>
wrote:

> Thanks for the reply.
> But it did not work for me. Can you please write the command line, it would
> be much helpful.
> Thank you.
>
> On Thu, Aug 29, 2019 at 2:33 PM Mohammadreza Niknam Hamidabad <
> jj700physics at gmail.com> wrote:
>
> > Hi,
> > I'm currently using Gromacs 2018 and I'm not quite sure about the 5.x
> > version. The gyrate module doesn't have -tu flag so my suggestion is that
> > you convert your .xtc file to a new xtc file with trjconv -tu ns then use
> > gyrate for your calculation.
> > I hope you find it useful.
> >
> > Best regards,
> > Reza
> >
> >
> > On Thu, Aug 29, 2019 at 7:38 AM sudha bhagwati <sudhabhagwati at gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> I am using the GROAMCS 5.1.4 version.
> >>
> >>
> ----------------------------------------------------------------------------------------------------------------------------------------
> >> Running the commands below:
> >>
> >>
> >> *gmx gyrate -s md_0_20.tpr -f md_0_20_noPBC.xtc -o gyrate.xvg -tu ns*
> >> *OR*
> >> *gmx energy -f ie.edr -o interaction_energy.xvg -tu ns*
> >>
> >>
> >> Error while executing commands:
> >>
> >> *Error in user input:*
> >>
> >> *Invalid command-line options    Unknown command-line option -tu*
> >>
> >>
> ----------------------------------------------------------------------------------------------------------------------------------------
> >>
> >> I want to generate my plots for nanosecond scale. Could you please help
> me
> >> out with this issue. I'd be really grateful to you.
> >>
> >> Thank you.
> >>
> >>
> >> --
> >> Thanks & regards
> >> ~
> >> Sudha Bhagwati
> >> --
> >> 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-request at gromacs.org.
> >>
> >
>
> --
> Thanks & regards
> ~
> Sudha Bhagwati
> --
> 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-request at gromacs.org.
>