[EMAIL PROTECTED] wrote:
Please don't post to the users list and the developers list
simultaneously with the same question. I think this is more
appropriately a users list question. I guess if you also get a reply on
the developers list then it pays to post to both, but the idea is to put
it only in one space.
Hi
For one molecule, will Gromacs give the same set of force field
parameters to this molecule no matter this molecule is put in water or
in vacuum?
The bond length, the bond angle, and the dihedral angles of the same
molecule will be different in water and in vacuum.
So, will the force field parameters be changed/ adjusted in water than
in vacuum?
The parameters themselves will be the same in water or in vacuum.
However, the behaviour of a molecule will be entirely different in water
or in vacuum since vacuum lacs the hydrophobic effect that falls out of
water being in the system. The hydrophobic effect is, in my opinion, one
of the great success stories of MD. On the other hand, proteins will
change their structure much faster in vacuum since the friction is much
less in that case. So if you are looking to generate structures for some
other purpose without caring if the sampling itself is Boltzmann (e.g.
generating structures for use with the ENSEMBLE program to characterize
intrinsically unfolded proteins by Dr. Julie Forman-Kay) then in vacuuo
may be the best way to go.
Actually in our experience this is not the case. In vacuum the proteins
collapse and do hardly move away from this structure. See
Biochemistry 46 pp. 933-945 (2007)
JPCB 111 pp. 13147-13150 (2007)
JACS 129 pp. 6726-6735 (2007)
Int. J. Mass Spectrom. 248 pp. 124-135 (2006)
How does Gromacs set the force field parameters for the molecule?
Based on the forcefield that you choose in pdb2gmx
I mean..... are the force field paramters determined in local or in
global?
local
Could I change parts of the force field parameters which I found from
the published paper?
You _could_, but then you would be doing something entirely new and you
should explain everything in your publication.
Or, I could not change parts of the force field parameters; instead, I
have to change the whole set of the force field
parameters???
I think nearly everyone that you talk to would say that by changing
_any_ part of the ff parameters then you are de-facto changing _all_ of
the ff parameters since it is one interconnected set. I personally am
not convinced that this is always the case. For example, I am not
convinced that protein ff parameters are in any way tied to DNA ff
parameters, even if they are generated consistently. But this is a
minority view any you are most secure if you consider a ff as a single
unmodifiable entity.
BTW your post did not give any hint at what you are trying to do. I am
sure that you don't want to be scooped, but it is difficult to give any
assistance when you do not say what your goal is.
Chris.
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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