[gmx-users] after extending simulation

[Andrea Spinelli]

I don’t obtain a .gro file after each extension.
What is wrong?

On Jul 9, 2015, at 8:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 
> 
> On 7/9/15 2:10 PM, Andrea Spinelli wrote:
>> So, I’m ok!
>> I can read the only one .gro file created at the first simulation as the final .gro file after all extensions. That’s right?
>> 
> 
> No, you should get a .gro file at the end of each run.  But that's missing out on most of the information; loading the trajectory is of course more informative than any single snapshot.
> 
> -Justin
> 
>> 
>> On Jul 9, 2015, at 7:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 
>>> 
>>> 
>>> On 7/9/15 1:49 PM, Andrea Spinelli wrote:
>>>> I’m sorry, I miss something with cut and paste command.
>>>> On terminal I wrote:
>>>> 
>>>> gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr
>>>> gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt
>>>> 
>>>> There is no gromacs coordinate file in VMD, I have to convert a md_0_2.tpr into try or try file?
>>>> 
>>> 
>>> The contents of md_0_1.tpr and md_0_2.tpr are identical except that the latter contains a different number of steps.  When providing mdrun with a .cpt file, it carries out the run from that point, so the starting point of the run (time = 0) is always the same.
>>> 
>>> The final coordinates are always written to a .gro file unless you specify a different format (which your above command does not).  Whatever that file is called depends on the first run (md_0_1), because the file names are stored in the .cpt file; they will be appended to by default.  The final .gro file has an appended name rather than being overwritten, IIRC.
>>> 
>>> -Justin
>>> 
>>>> On Jul 9, 2015, at 7:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>> 
>>>>> 
>>>>> 
>>>>> On 7/9/15 1:25 PM, Andrea Spinelli wrote:
>>>>>> Dear all,
>>>>>> I extend a simulation (GROMACS 5.0.5) with these command lines:
>>>>>> 
>>>>>> convert-tpr -s md_0_1.tpr -extend 1000 -o next.tpr
>>>>>> mdrun -s md_0_2.tpr -cpi md_0_1.cpt
>>>>>> 
>>>>>> And now?
>>>>> 
>>>>> Well, the above sequence of commands won't do anything because (1) it's "gmx convert-tpr" not just "convert-tpr" and (2) if you create "next.tpr" and try to run "md_0_2.tpr" then mdrun will exit.
>>>>> 
>>>>>> What I have to do to view the new .gro file (i use VMD to see it) with new state of protein folding simulation?
>>>>> 
>>>>> Load it like any coordinate file.
>>>>> 
>>>>> -Justin
>>>>> 
>>>>> --
>>>>> ==================================================
>>>>> 
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>> 
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>> 
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>> 
>>>>> ==================================================
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>>>>> Gromacs Users mailing list
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>>>> 
>>>> Andrea Spinelli
>>>> 
>>>> Please do not print this email unless really need to.
>>>> Save paper, save trees, save space, save money - life matters.
>>>> 
>>> 
>>> --
>>> ==================================================
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>> 
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>> 
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>> 
>>> ==================================================
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>>> Gromacs Users mailing list
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>> 
>> Andrea Spinelli
>> 
>> Please do not print this email unless really need to.
>> Save paper, save trees, save space, save money - life matters.
>> 
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==================================================
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
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Andrea Spinelli

Please do not print this email unless really need to.
Save paper, save trees, save space, save money - life matters.