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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--
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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