[gmx-users] trjcat set timestep/amb2gmx?

[Steven Neumann]

Got this.

Thank you


On Tue, Apr 16, 2013 at 11:21 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/16/13 5:32 AM, Steven Neumann wrote:
>
>> Thank you all.
>>
>> Would you suggest any link to a script like amb2gmx.pl ? I cannot fina
>> anything like this - basically I wish to convert top.prmtop to top.tpr.
>>
>>
>>
> You will not be able to produce a .tpr file directly.  The amb2gmx script
> simply converts the prmtop to a .top file, which can then be input into
> grompp.
>
> -Justin
>
>
>
>>
>> On Tue, Apr 16, 2013 at 9:26 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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