[gmx-users] Re: tpbconv extension

[ram bio]

Hi Berk,

Thanks for the suggestion, does the tpr file generated by the options
mention on PC would work on a server with older version of Gromacs
i.e. 4.0...

Ram

On Mon, Dec 13, 2010 at 6:04 PM, Berk Hess <gmx3 at hotmail.com> wrote:
> Sorry, I mistook a million ps for a millisecond, this is a microsecond.
> The maximum number of steps in version 4.0 is INT_MAX, which is
> 2,147,483,647.
> From the name of your tpr file it seems you are not exceeding this,
> so I don't know what's wrong exactly.
>
> But for this reason (and many other reasons), you might want to consider
> upgrading to 4.5.3 (and possibly applying the bug-fix I mailed before).
>
> Berk
>
>> Date: Mon, 13 Dec 2010 17:56:43 +0100
>> Subject: Re: [gmx-users] Re: tpbconv extension
>> From: rmbio861 at gmail.com
>> To: jalemkul at vt.edu; gmx-users at gromacs.org
>> CC:
>>
>> 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
>> >>>
>> >>> ========================================
>> >>> --
>> >>> gmx-users mailing list    gmx-users at gromacs.org
>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>> Please search the archive at
>> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> >>> Please don't post (un)subscribe requests to the list. Use the www
>> >>> interface
>> >>> or send it to gmx-users-request at gromacs.org.
>> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>>
>> >>
>> >
>> > --
>> > ========================================
>> >
>> > 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
>> >
>> > ========================================
>> > --
>> > gmx-users mailing list    gmx-users at gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > Please don't post (un)subscribe requests to the list. Use the www
>> > interface
>> > or send it to gmx-users-request at gromacs.org.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>