But, if I understood well, iwrap doesn't resolve the high diffusion of
the protein in the box (and I proved with iwrap=1 too). So, the only
solution is to enlarge the box size? Is there any other possibility?
Thanks,
Fernando
On Wed, 8 Aug 2012 12:13:51 +0200, Jérôme Golebiowski wrote:
> If you are performing an umbrella sampling and this extends your
> molecule to
> larger value than your box size, you should enlarge your box.
> Otherwise, maybe just setting iwrap to 1 will help keeping the
> protein close to
> the box center.
> HTH.
> Best,
> Jerome
>
>
>
> Selon Fernando MartÃn GarcÃa <fmgarcia.cbm.uam.es>:
>
>> Dear Amber users,
>>
>> I have a "technical" problem with a distance restraint. I'm working
>> with a protein with a 12 angs. TIP3 box. The simulation time is 30
>> ns.
>> After 20 ns, a small part of the protein is out of the box. The
>> problem
>> is that one of the residues out of the box has a restrain with one
>> residue in the part of the protein inside the water box, so the
>> value
>> changes, what it causes a high restraint value. Is there any
>> solution
>> for this?
>>
>> Thanks
>> --
>> ==============================================
>> Fernando MartÃn GarcÃa
>> Molecular Modelling Group - Lab 312.1
>> Molecular Biology Center "Severo Ochoa"
>> C/ NICOLáS CABRERA, 5.
>> UAM University. Cantoblanco, 28049 Madrid. Spain.
>> TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
>> Web: http://fertoledo.wordpress.com/
>> ==============================================
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> --
> Jérôme Golebiowski
> Institute of Chemistry - Nice
> Molecular Modeling Team
> UMR 7272 CNRS, University of Nice Sophia Antipolis
> 06108 Nice cedex 2, France
>
> tel: +33 (0)4 92 07 61 03
> http://www.unice.fr/icn
> http://www.unice.fr/icn/golebiowski
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
==============================================
Fernando Martín García
Molecular Modelling Group - Lab 312.1
Molecular Biology Center "Severo Ochoa"
C/ NICOLáS CABRERA, 5.
UAM University. Cantoblanco, 28049 Madrid. Spain.
TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
Web: http://fertoledo.wordpress.com/
==============================================
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Received on Wed Aug 08 2012 - 04:00:04 PDT
