[gmx-users] amyloid simulation in water+glucose

[David]

On Tue, 2003-09-02 at 18:27, Aswin Narain wrote:
> Hi all
> 
> As a relative new-bie to gromacs I did not really
> understand the reply. But then, the energy
> minimization that I tried was a flop as well. The
> result was: converged to machine precision. Step size
> too small. 
> A more detailed answer will be really helpful!

start with a single molecule
minimize the structure
build a box with genconf
fill the box with water using genbox
minimize
simulate

check after each step whether it went well (e.g. check energy components
after minimize)

> 
> 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 and Molecular 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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