[gmx-users] amyloid simulation in water+glucose

[David van der Spoel]

On Tue, 2003-09-02 at 15:09, Aswin Narain wrote:
> Hi all
> 
> I am trying to simulate a peptide in water containing
> glucose. I got the glucose topologies using PRODRG.I
> put the glucose (nmol=20) using genbox. But during the
> md, I faced problems: cannot fix pbc.
> How doI go about correcting this. A detailed answer
> will help.
Are you sure the overall density is OK?

Then start with  energy minimization of your box followed by constant
volume simulation, and finally constant pressure with very weak coupling
(5 ps)

> 
> Thanks
> 
> Aswin
> 
> =====
>  Aswin Sai Narain. S
> Student
> Centre for Biotechnology
> Anna University
> Chennai 25
> Residence
> 20, 3rd main road
> Nanganallur
> Chennai 61
> 
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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