[gmx-users] Re: tpbconv extension

[Justin A. Lemkul]

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

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