Mark Abraham wrote:
Egidijus Kuprusevicius wrote:
Dear users,
from PRODRG beta server I have got a very big c1 parameter in my
topology file is that normal or smth is wrong with my topology?
[ angles ]
; ai aj ak fu c0, c1, ...
....
17 19 21 2 120.0 505.0 120.0 505.0 ; CAH CAD CAP
20 19 21 2 120.0 505.0 120.0 505.0 ; HAD CAD CAP
19 21 22 2 120.0 560.0 120.0 560.0 ; CAD CAP CAC
19 21 24 2 120.0 560.0 120.0 560.0 ; CAD CAP CAE
22 21 24 2 120.0 *560.0* 120.0 *560.0* ; CAC CAP CAE
21 22 23 2 180.0 *41840001.2* 180.0 *41840001.2 ;* CAP CAC NAB
21 24 25 2 120.0 *505.0* 120.0 *505.0 ;* CAP CAE HAE
21 24 26 2 120.0 505.0 120.0 505.0 ; CAP CAE CAI
25 24 26 2 120.0 505.0 120.0 505.0 ; HAE CAE CAI
16 26 24 2 120.0 505.0 120.0 505.0 ; CAR CAI CAE
You'll notice that this angle is linear - angle 180 degrees. (If you
don't know how to read these lines, consult the table in Chapter 5 of
the manual.) A large force constant would prevent any deviation from
linear, which I can imagine is right for some weirder chemical species.
An angle of 180 is ill defined, that is, the force is undefined. The
energy will be fine. Using a large force constant will make certain that
your system crashes. You should consider using virtual sites instead.
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.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
--
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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list [email protected]
http://www.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
