[gmx-users] -t option?

[Peter Kroon]

Hi Hadi,


to expand a little on Mahdi's (correct) answer:

The checkpoint file contains coordinates and velocities in full
precision (unlike .gro and .xtc files). In addition, it contains the
state of the thermostat and barostat (if applicable). The
thermo/barostat states are not present in the gro/mdp/tpr files, since
they depend on the history of your system. Because of this, including
the checkpoint file to continue your simulation is always a good idea.

See also: `gmx mdrun -h` and `gmx grompp -h`.


Peter

On 19-09-19 05:13, Hadi Rahmaninejad wrote:
> Thanks Mehdi,
>
> Best,
> Hadi
>
> On Wed, Sep 18, 2019 at 12:38 PM Mahdi Bagherpoor <mehdi.bpour at gmail.com>
> wrote:
>
>> Hi Hadi,
>>
>> It is well explained in Gromacs tutorial, in the below:
>> http://www.mdtutorials.com/gmx/lysozyme/07_equil2.html
>>
>> "Note that we are now including the -t flag to include the checkpoint file
>> from the *NVT* equilibration"
>>
>> Cheers,
>> Mahdi
>> On Wed, Sep 18, 2019 at 5:43 PM Hadi Rahmaninejad <ha.rahmaani at gmail.com>
>> wrote:
>>
>>> Hello dear users,
>>>
>>> I am going to run a simulation according to a tutorial, but there is an
>>> option of "-t nvt.cpt" that I don't know what is it, and I couldn't find
>>> any explanation for that. I appreciate if any of you can give me a short
>>> description of what is that doing,
>>>
>>> Best wishes,
>>> Hadi
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