[gmx-users] g_traj time unit

[Chandan Choudhury]

On Fri, Mar 28, 2014 at 4:27 PM, Tegar Nurwahyu Wijaya <
tnurwahyuwijaya at gmail.com> wrote:

> Thanks for the reply.
>
> I had a 1 ms simulation and I want g_traj to give the time in ns in the xvg
> output file. Instead of give me 1000 ns in the x axis, g_traj gave 1000000
> ns. I checked it with xmgrace. It seems g_traj only change the label and
> did not convert the original time (ps) to ns as I wanted.
>

Use  -tu ns

Chandan

> On Mar 28, 2014 4:56 PM, "X Rules" <xrules at live.com> wrote:
>
> >
> > Hi,
> >  Is it not that g_traj asks you if you have a different time unit in your
> > trr file. by default it is written in ps. So if you say here ns, then, it
> > means 1000 ps. Which is why all your values are multiplied by 1000. What
> > does your plot axis say when you open your xvg file?  What are the time
> > units there?
> >
> >
> >
> > > Date: Fri, 28 Mar 2014 16:27:23 +0700
> > > From: tnurwahyuwijaya at gmail.com
> > > To: gmx-users at gromacs.org
> > > Subject: [gmx-users] g_traj time unit
> > >
> > > Dear GROMACS users,
> > >
> > > I tried to extract box information from my simulation using the
> following
> > > command.
> > >
> > > g_traj -f dopc-dppc_noW.trr -s topol.tpr -ob box_dopc-dppc.xvg -tu ns
> -b
> > 0
> > > -e 1000
> > >
> > > I expected to have 1000 ns as the maximum value on the x (time) axis.
> > > However I got 1000000 as the maximum value. Then I tried the following
> > > command.
> > >
> > > g_traj -f dopc-dppc_noW.trr -s topol.tpr -ob box_dopc-dppc.xvg -tu ns
> -b
> > 0
> > > -e 100
> > >
> > > Here I got 100000 as the maximum value. It seems g_traj failed to
> convert
> > > the time unit from the trajectory value (ps) to ns as indicated in the
> > > command. However g_traj successfully recognize the end of the
> trajectory
> > to
> > > be read exactly as I indicated in the commands above.
> > >
> > > Is there any mistake in my commands or this is a bug of g_traj?
> > >
> > > Thanks,
> > > Tegar
> > > --
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-- 

--
Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India