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

[David van der Spoel]

chris.neale at utoronto.ca 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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se