[gmx-users] NM and minimisation problems

[David van der Spoel]

On Wed, 2004-02-11 at 12:41, Nguyen Hoang Phuong wrote:
> > I try to do a normal mode analysis of a molecule. What interest me is just a part I suppose to be a hinge.
> > what are the settings I have to disable in the .mdp file to run it smoothly?
> 
> Hi,
> 
> first, you should have a look at the top file, if you see something like
> 
> ; Include water topology
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
> 
> then you can try with this file:
> 
> 
> title                    = xxxx
> cpp                      = /lib/cpp
> include                  = -I../top
> define                   = -DFLEX_SPC

I would like to point out that tis has been changed a bit in 3.2
If you use spc water this still will work, but for other models the more
generic way of writing is:

#include "water.itp" (either tip3p, tip4p, spc, spce)

define = -DFLEXIBLE


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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