Shuangxing Dai wrote:
Hi, all,
I was wondering if the shell molecular dynamics exclude the
electrostatic interaction automatically. According to the shell model,
the interaction between core and shell in replaced by the harmonic
interaction. If not, how to exclude electrostatic interaction between them?
To know what happens you can check the list of exclusions in the tpr
file using gmxdump. Then you can decide whether or not it is necessary
to add an exclusion manually.
If I define in the top file:
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
2 1 no
1.0 1.0
[ atomtypes ]
;name at.num mass charge ptype a
b c
O 8 15.99940 0.040 A 0.00000E-00
0.00000E-00 0.00000E-00
OS 8 0.00000 -2.040 S 0.00000E-00
0.00000E-00 0.00000E-00
ZN 30 65.37000 2.000 A 0.00000E-00
0.00000E-00 0.00000E-00
[ nonbond_params ]
; i j func a b c
OS OS 2 9.21239E+05 4.56287E+01 3.08753E-03
OS ZN 2 5.11083E+04 2.79251E+01 0.00000E+00
ZN ZN 2 0.00000E+00 1.00000E+02 0.00000E+00
OS is shell and O is core for oxygen.
Thanks,
*/Shuangxing Dai/*
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[email protected] [email protected] http://folding.bmc.uu.se
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
