[gmx-users] after extending simulation

[Justin Lemkul]

On 7/9/15 2:16 PM, Andrea Spinelli wrote:
> I don’t obtain a .gro file after each extension.
> What is wrong?
>

No idea, only you can see your files and their time stamps.

Pro tip: use -deffnm to always get different file names.  I never append using 
mdrun and this is foolproof (e.g. extending as you are, but with slightly 
different names):

gmx mdrun -deffnm md_1_2.tpr -cpi md_0_1.tpr

The nomenclature makes it trivial to loop in a bash script to let the run go as 
long as you like without manual intervention.

-Justin

> 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
>>>>>>
>>>>>> ==================================================
>>>>>> --
>>>>>> 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.
>>>>>
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> 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.
>>>
>>
>> --
>> ==================================================
>>
>> 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
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
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>>
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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

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