[gmx-users] pbc=full in 3.3.2

[Jay McAliley]

Thanks, Berk,

I'll check out 3.3.3 from CVS then.

Jay

Berk Hess wrote:
> Hi,
>
> I have not checked what causes this problem,
> but it seems to have been fixed for version 3.3.3.
>
> Berk.
>  
>
>   
>> Date: Tue, 26 Feb 2008 12:48:10 -0500
>> From: mcalilj at CLEMSON.EDU
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] pbc=full in 3.3.2
>>
>> Sorry for the double post but I forgot my descriptive title...
>>
>>
>>
>> Hi,
>>
>> I am having a problem using pbc=full for crystalline polymers on Gromacs
>> 3.3.2.
>> I have input files that run in 3.3.1 with no problem, but the system
>> explodes in 3.3.2.
>>
>> Here's a simplified cartoon of my system, dotted lines being box boundaries:
>>
>>       (CH3)  (CH3)
>>    ....|......|....
>>    .   CH     CH  .
>>    .  / \    / \  .
>> (C)--O   C--O   C--(O)
>>    .    ||     || .
>>    .     O      O .
>>    .              .
>>    .   CH3    CH3 .
>>    .   |      |   .
>>    .   CH     CH  .
>>    .  / \    / \  .
>> (C)--O   C--O   C--(O)
>>    .    ||     || .
>>    .     O      O .
>>    .              .
>>    .   CH3    CH3 .
>>    ....|......|....
>>       (CH)   (CH)
>>
>> The system blows up, beginning with the carbons and oxygens in the periodic
>> images (shown in parentheses). Hydrogens initially stay put. All bonds that
>> cross the box boundary seem to lengthen; it's as if those bonds were defined
>> between the in-box atom positions, and they are pulling the atoms together
>> (each toward the center of the cell). It happens for the side group bonds as
>> well as the main chain bonds that define the infinite chains.
>>
>> I won't say I'm positive I have my topology right.. but has anyone been
>> using pbc=full in 3.3.2?
>>
>> I made a tarball of my input files if anyone is willing to take a look:
>> http://people.clemson.edu/~mcalilj/pbcfull.tar.gz
>> On our hardware these run ok for 3.3.1 but crash in 3.3.2.
>>
>> Thanks for your help,
>>
>> Jay McAliley
>>
>>
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