[gmx-users] trjcat set timestep/amb2gmx?

[Steven Neumann]

I read it... did not know styles are equal to points :)


On Wed, Apr 17, 2013 at 4:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/17/13 11:06 AM, Steven Neumann wrote:
>
>> What do you mean by style 8?
>>
>>
> Did you read trjconv -h?  There's an enumerated list in the very
> beginning. Mark is pointing you towards #8 in that list.
>
> -Justin
>
>
>
>> On Tue, Apr 16, 2013 at 4:51 PM, Mark Abraham <mark.j.abraham at gmail.com>*
>> *wrote:
>>
>>  See style 8 for trjconv -h
>>>
>>> Mark
>>>
>>>
>>> On Tue, Apr 16, 2013 at 10:26 AM, francesco oteri <
>>> francesco.oteri at gmail.com
>>>
>>>> wrote:
>>>>
>>>
>>>  Hi,
>>>> yes Marc you are right but the last time I used gromacs on a namd
>>>> trajectory
>>>> I noticed that time in the output files is useless 'cause it is always
>>>> 0.
>>>> I understand that, since this information is usually took from .trr or
>>>> .xtc, it cannot
>>>> be extracted from a .dcd, but it could be more useful using as x the
>>>>
>>> frame
>>>
>>>> number.
>>>> This could, at least, permitting to visualize the plot with xmgrace
>>>>
>>> without
>>>
>>>> postprocessing
>>>> the .xvg
>>>>
>>>>
>>>>
>>>> Francesco
>>>>
>>>>
>>>> 2013/4/16 Mark Abraham <mark.j.abraham at gmail.com>
>>>>
>>>>  On Apr 15, 2013 6:27 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 4/15/13 12:23 PM, Steven Neumann wrote:
>>>>>>
>>>>>>>
>>>>>>> Dear Gmx Users,
>>>>>>>
>>>>>>> I obtained dcd trajectory from simulation in another software. I
>>>>>>>
>>>>>> wish
>>>
>>>> to
>>>>
>>>>> merge many trajectories using trjcat with a proper timestep. Is that
>>>>>>>
>>>>>> option
>>>>>
>>>>>> possible using gromacs or shall use a script to produce tpr file
>>>>>>>
>>>>>> from
>>>
>>>> my
>>>>
>>>>> prmtop file e.g. amb2gmx ? Any links for such a script?
>>>>>>>
>>>>>>>
>>>>>> If you linked against VMD libraries when installing, Gromacs can
>>>>>>
>>>>> handle
>>>
>>>> any trajectory/coordinate file format that VMD can, thus requiring no
>>>>> conversion. If you need a .tpr file to do the analysis you are trying
>>>>>
>>>> to
>>>
>>>> do, then yes, you need to convert topology information into the proper
>>>>> format.
>>>>>
>>>>> ...and be aware that a -s option that accepts both .tpr and (say) .gro
>>>>> formats (as shown in g_tool -h) might succeed with the latter if only
>>>>>
>>>> atom
>>>>
>>>>> names, rather than (say)  bonding connectivity is required for g_tool
>>>>>
>>>> to
>>>
>>>> work.
>>>>>
>>>>> Mark
>>>>>
>>>>>> -Justin
>>>>>>
>>>>>> --
>>>>>> ==============================**==========
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Research Scientist
>>>>>> Department of Biochemistry
>>>>>> Virginia Tech
>>>>>> Blacksburg, VA
>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>>>>
>>>>>> ==============================**==========
>>>>>>
>>>>>> --
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>>>>
>>>>
>>>> --
>>>> Cordiali saluti, Dr.Oteri Francesco
>>>> --
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> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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