[gmx-users] Re: gmx-users Digest, Vol 27, Issue 35

David van der Spoel spoel at xray.bmc.uu.se
Wed Jul 12 12:24:42 CEST 2006

On Wed, 12 Jul 2006, pim schravendijk wrote:

>Consider a pair of spherical macromolecules of diameter ~2.5 nm,
>> arranged along an x-axis so that their centres of mass are 4nm apart,
>> then centered in a 14 x 10 x 10 nm periodic box,
>The box is then filled with TIP4P water, energy minimized, run with
>> nsteps              =  1000000  ; total 1000 ps.
>> The problem is that when I run this simulation, the expected drift of
>> the macromolecules towards each other does not occur.
>This is a huge system! How many water molecules do you have? What is the
>experimental diffusion constant of these particles in water? In any case, in
>1 ns you probably won't see much happening there. I guess in 10 / 100  ns
>you won't see much drift happening as well. Probably you need some form of
>distance dependent free-energy (e.g. distance constaints) method to get any
>wiser about the drift of the molecule
I agree. Try some form of potential of mean force, by computing the 
effective force at different distance. The largest problem is 
the rotational equilibration of the macromolecules. You may try to look 
into the pull code options.

David van der Spoel, PhD, Assoc. 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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