[gmx-users] Fene and Quartic Potential

[David van der Spoel]

PAUL NEWMAN wrote:
> Dear all:
> 
> I want to use Fene Potential and Quartic Angle Potential which both are available in the new gromacs version 
> 3.3 . What I want to know is how can I  set up the parameters for these potential in my *.itp file. Ok my try is here. Are the possition of the parameters  ok? and Are the number of functs ok for boht Fene and quartic?. I took the information from the manual reference 
> 3.3 ( page 97 ). Thanks in advance.
I don't really know, but you can check for yourself by running
gmxdump -s topol.tpr | less
and checking for the parameters used for these potentials (search by 
typing /idef)

> 
> ;FORCE FIELD  FOR POLYELECTROLYTES WITH COUNTERIONS 
> 
> [ defaults ]
>  1       2
> 
> [ atomtypes ]
> ; name  bond_type    mass    charge   ptype     sigma      epsilon
> 
> [ nonbond_params ]
> ; i    	j	funda       sigma          epsilon 
>      
> 
> ;;COUNTERIONS
> 
> [ moleculetype ]
> ; molname       nrexcl
> 
> [ atoms ]
> ;id type resnr residu  atom  cgnr   charge
>  
> ;;POLYELECTROLYTE 
> 
> [ moleculetype ]
> 
> 
> ; molname       nrexcl
> 
> [ atoms ]
> ;id    type  resnr   residu    atom     cgnr  charge
>  
> [ bonds ] ; FENE potential
> ;  i   j
> funct   bo      kb
>    1   2  7      2        7
> 
> [ angles ] ; QUARTIC ANGLE potential
> 
> ; i  j  kfunct th0  C0  C1  C2  C3  C4
>   1  2  3  
> 6   180   0   0   5   0   200
> 
> 
> -- 
> Cheers,    
>       
> Paul
> National Tsing Hua University (清華大學)
> 
> 謝謝你的幫忙
> I appreciate your help. Thanks!
> Os agradezco la ayuda. Gracias!
> 
> 
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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