[gmx-users] helices, again

[David]

On Tue, 2003-07-15 at 21:57, Nagy, Peter I. wrote:
> Dear Gromacs Users!
> 

>   Thus it seems to me that the coordinates were modified by 2Bz for
> helix1, and by (1By + 1Bz) for helix2. Then I am not surprised that
> when
> I performed an MD and checked the motion in ngmx, my double helix
> seemed to
> have fallen apart. The very likely reason is a coordinate
> transformation
> throughout the energy minimization. The minimization process itself
> probably works correctly, because the coordinate changes only by up to
> 0.01 nm, and the rude change is a consistent translation along the y
> and z axes. But what did cause it?

The algorithm just takes the first atom and puts it in the central box,
then makes a continuus molecule from that, which means that all but one
atom can be outside the box. This is harmless in itself, and you can
verify that your structure is unchanged by e.g. checking the
intermolecular hydrogen bonds before and after minimization (with
g_hbond). However your box might still be too small.

> 
>   For safety, I enclose the emgas.mdp file below:
> 
> title               =  cpeptide
> cpp                 =  /lib/cpp
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002    ; ps
> nsteps              =  1000
> nstlist             =  10
> ns_type             =  grid
> rlist               =  0.9
> rcoulomb            =  0.9
> rvdw                =  0.9
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  100.0
> emstep              =  0.01
> 
> 
> Thanks for any help
> 
> Peter Nagy
-- 
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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