[gmx-users] g_traj time unit

[Justin Lemkul]

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

==================================================