On Fri, 4 Jan 2008, Maik Goette wrote:
Hi
I just found a strange behaviour of GROMACS, when processing topologies with
B-values. Maybe I just think of it as unintuitive/bug, but here we go:
e.g. OPLS
Consider an angle given (all atoms have B-values, which angle-parameter can
be found by GROMACS in the bonded.itp for the A- and B-state):
Original topology entry:
10 12 14 1
Manually edited entry (with the correct ff-term):
10 12 14 1 109.700 669.440
Now, a dump from the tpr-files yields the following:
Original:
functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02,
ctB= 2.92880e+02
Edited:
functype[109]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02,
ctB= 6.69440e+02
Now, what obviously happens is, that GROMACS searches the entries of the
angle in the FF for both states and uses them in the case of the original
topology.
If one puts a manual entry into the topology for the A-state though, the
B-state is simply copied, instead of searched by GROMACS.
This, IMHO, is quite inconvenient. Is this a bug or a feature?
it cannot be called as a bug... when you mention parameters for A state
in topology explicitly then grompp will expect you to mention the B state
parameters also, and if it doesn't find it, it will assign A state
parameter to B state. that is quite well documented, i think, in manual.
So there is no reason to think it as a bug.
bharat
Regards
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
_______________________________________________
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
