[gmx-users] Re: tpbconv extension

[ram bio]

Hi Justin and Berk,

Thanks for the suggestions.

I am using gromacs 4.0.7 single precision, and would like to extend my
run each time by 1 microsec as it fits into the wall time on the
server for my system.
Please suggest.

Thanks
Ram
On Mon, Dec 13, 2010 at 5:40 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> ram bio wrote:
>>
>> Hi Justin,
>>
>> The command was:
>>
>> tpbconv -s memb12extnr42000ns.tpr -extend 1000000 -o
>> memb12extnr43000ns.tpr
>>
>
> Try using -nsteps instead.  There are issues with -extend and -until (bad
> rounding, limits to the size of the number, etc) that can cause this
> problem.  I believe all of this has been resolved as of Gromacs 4.5, for
> future reference.
>
> -Justin
>
>> Thanks
>>
>> Ram
>>
>> On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>
>>> ram bio wrote:
>>>>
>>>> Dear Gromacs users,
>>>>
>>>> I am running a CG simulation for a peptide in lipid bilayer, and the
>>>> run didnot extend after 42000 ps using gromacs 4.0.7,
>>>>
>>>> Reading toplogy and shit from memb12extnr42000ns.tpr
>>>> Extending remaining runtime of by 1e+06 ps (now -2144967266 steps)
>>>> You've simulated long enough. Not writing tpr file
>>>>
>>>>  Please give your suggestions to overcome this error.
>>>>
>>> What was your command?
>>>
>>> -Justin
>>>
>>>> Ram
>>>>
>>>>
>>>>
>>>>
>>>> On Mon, Dec 13, 2010 at 5:26 PM, ram bio <rmbio861 at gmail.com> wrote:
>>>>>
>>>>> Dear Gromacs users,
>>>>>
>>>>> I
>>>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> 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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>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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