[gmx-users] Force field parameters in water or in vacuum?

[chris.neale at utoronto.ca]

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.

> 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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