[gmx-users] improper force constants

[David]

On Sat, 2003-06-14 at 10:36, Daan van Aalten wrote:
> Hi PeiQuan
> 
> We have deliberately increased the force constants on the impropers
> 10-fold to make the geometry of GMX mimimized molecules better agree
> with known small molecule structures from the CSD.
> In fact we are considering introducing an entirely new set of forcefield
> constants based on small molecule crystal structure databases.
> 
You should be careful to not only look at structure but also at
frequencies of out of plane vibrations. If you make the force constant
ten times bigger, the frequency of that motion will also become higher
(by sqrt 10 IIRC). Is that physical? Of course GROMOS has only 2 values
for force constants in all systems, so that is not very realistic
either, but if you're going to change it better check whether these
frequencies make any sense. It is also rather straightforward to get
them from quantum calculations, or you could e.g. check another force
field...


> cheers
> 
> Daan
> 
> On Sat, 14 Jun 2003, PeiQuan Chen wrote:
> 
> > Dear Daan van Aalten:
> >
> >   Thank you for kind help.
> >   But I have something confused with the topol files generated by PRODRG.
> > The dihedrals parameters I get from the PRODRG is following:
> >  [ dihedrals ]
> >  ;ai  aj  ak  al  fu    c0    c1 m  c0   c1 m
> >    1   2   3   4   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAA  CAB  CAD  CAF
> >    2   3   4   5   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAB  CAD  CAF  CAE
> >    3   4   5   6   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAD  CAF  CAE  CAC
> >    4   5   6   1   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAF  CAE  CAC  CAA
> >    5   6   1   2   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAE  CAC  CAA  CAB
> >    6   1   2   3   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAC  CAA  CAB  CAD
> >
> > But From the ffgmxbon.itp, I have found that:
> > [ dihedraltypes ]
> >   ; i    l func        q0          cq
> >  CR61 CR61    2     0.000     167.360
> >
> >    So the topol files generated by PRODRG is not consistent with the ffgmxbon.itp. Is it a bugs?
> >
> >
> > Sincerely yours
> > ----
> > PeiQuan Chen
> > ________________________________________________________________________
> > PeiQuan Chen 	Department of Chemistry, Nankai University
> > WeiJin Road 94, TianJin, 300071, P.R.China
> > phone:	(86)2223506728		Mobile Phone: (+86)13920675030
> > gromacs at 163.com
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
> 
> 
> ##############################################################################
> 
> Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
> Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
> Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
> School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
> Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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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