[gmx-users] Inconsistent shifts using multiple bonds type 6

[TJ Piggot]

Hi

I see what you are saying, i will try and recompile with the changes you 
have suggested

Thanks you

Tom

--On Tuesday, March 06, 2007 14:07:36 +0100 Berk Hess <gmx3 at hotmail.com> 
wrote:

>
>
>
>> From: TJ Piggot <t.piggot at bristol.ac.uk>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] Inconsistent shifts using multiple bonds type 6
>> Date: Tue, 06 Mar 2007 12:44:16 +0000
>>
>> Hi Berk,
>>
>> Thanks for your reply. Yes the latter is the case in my system so i will
>> use pbc=full or remove these 'bonds' that i know will be greater than
>> half  of a box dimension
>
> You should remove those bonds, or make the box larger.
> pbc=full will work, but the distance vector will change to different
> periodic images when an "inter"-molecular periodic image distance
> becomes shorter than the true intramolecular distance.
>
> I assume your molecule is properly connected by normal bonds.
> A real fix would then be adding
> i!=F_HARMONIC &&
> to the if statement on line 272 of src/gmxlib/mshift.c
> and recompiling Gromacs, such that the harmonic potentials
> are not put into the graph.
>
> Berk.
>
> _________________________________________________________________
> Hotmail en Messenger on the move http://www.msn.nl/services
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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/mailing_lists/users.php



----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.