Re: SMD in water

From: Axel Kohlmeyer (
Date: Thu Jul 31 2008 - 09:16:01 CDT

On Thu, 31 Jul 2008, Roman Petrenko wrote:

RP> A general question about SMD and water.
RP> I've noticed in many articles that a protein is solvated and then SMD
RP> simulations are used (one atom fixed, another is pulled) without any
RP> boundary constraints.

RP> Is there any specific reason besides having significantly smaller
RP> number of water molecules?
RP> I want to simulate a small peptide with SMD (so the number of waters

the number of water molecules is always important. we always use
far too few waters (by orders of magnitude!) to not see any impact
of the number of waters.

RP> is not that important) and to use either cylindrical or spherical
RP> boundary conditions. The N- and C-terminal CA atoms are supposed to be

i would say that is running a very high risk of having your results
being dependend on the position of the peptide in the water area (you
have surface dipoles!). why not use periodic boundaries? you can use a
smaller box and the position of your peptide relative to the center of
the water system does not matter at all.

RP> pulled towards each other along parallel trajectories.
RP> Nterm------(force)------------------->
RP> \ ------
RP> --- / \ (peptide)
RP> \ / ---------
RP> ------- \
RP> <------------(force)-------------Cterm
RP> Does this design have an advantage that the whole peptide is always
RP> going to be at the center of either water sphere or water cylinder?

please note that this is not quite the same experiment than
pushing/pulling only one end. the pulling speed is usually
very high, so that the resulting free energy profile is not
the same. the area where you apply the pulling force is usually
behaving non-physical.

RP> The reason i ask is because maybe someone have already done this and
RP> ruled out this design as being not effective.

i cannot tell which option would be more effective, but you could
try it out with the SMD module for LAMMPS, that our group is working
on and that offers this functionality (and other enhancements).



Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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