[gmx-users] PBC in g_gyrate

[Erik Marklund]

Yes. Very true. By bad.

_______________________________________________
Erik Marklund, PhD student
Laborarory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, 	Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys

On Wed, 17 Jan 2007, Tsjerk Wassenaar wrote:

> Hi,
>
> I would say trjconv -pbc cluster sounds more appropriate.
>
> Cheers,
>
> Tsjerk
>
> On 1/17/07, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
>> Neither do I, to be honest, but you can always do a trjconv -pbc
>> nojump or something similar on your trajectory prior to analysis, just to
>> be sure.
>> _______________________________________________
>> Erik Marklund, PhD student
>> Laborarory of Molecular Biophysics,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3,   Box 596,        75124 Uppsala, Sweden
>> phone:  +46 18 471 4537         fax: +46 18 511 755
>> erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys
>> 
>> On Wed, 17 Jan 2007, singh wrote:
>> 
>> >
>> >
>> > Dear Gromacs users,
>> >
>> > I simulated 6 peptides in a cubical box. I want to calculate radius of
>> > gyration for all the peptides together (in order to get a rough idea 
>> whether
>> > they are coming together or not). But I am not sure whether g_gyrate 
>> takes
>> > into account Periodic boundary conditions while calculating radius of
>> > gyration for such a system.
>> >
>> >
>> >
>> > Regards,
>> >
>> > Gurpreet Singh
>> >
>> > -------------------------------------------------
>> >
>> > University of Dortmund
>> > Department of Chemistry
>> > Physical Chemistry I  -  Biophysical Chemistry
>> > Otto-Hahn Str. 6
>> > D-44227 Dortmund
>> > Germany
>> > Office:   C1-06 room 176
>> > Phone:  +49 231 755 3916
>> >
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>> >
>> > -------------------------------------------------
>> >
>> >
>> >
>> >
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>
>
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
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> The Netherlands
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