[gmx-users] trjcat set timestep/amb2gmx?

[Justin Lemkul]

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
>>>>>
>>>>> ========================================
>>>>>
>>>>> --
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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

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