[gmx-users] g_traj time unit

[Tegar Nurwahyu Wijaya]

I also did g_rms with time conversion routines and nothing strange
happened. It worked as I wanted. The problem arouse when I start using
g_traj.
On Mar 28, 2014 9:18 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 3/28/14, 6:57 AM, Tegar Nurwahyu Wijaya 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.
>>
>
> This is very strange.  The time conversion routines are not unique to
> g_traj; they are shared by numerous Gromacs tools.  Do other programs like
> g_hbond (or anything else that has -tu) show the same problem?
>
> -Justin
>
>  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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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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