Dear Dr.Schwieters,
Thank you for your response. I add those three lines before the high
temperature dynamics but the structures generated are still the same. Do you
have any suggestions?
Do you have some example scripts that deals with the similar problems to
share with?
Thanks
Best regards
Tiandi
Charles at Schwieters.org ???
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hello Tiandi--
> Since the structure of the protein and the tag are
> known, we want to group them during the simulation but
> not fix them. I know IVM (Dynamic Internal) is good
> for dealing this kind of problem. And PCS will be
> used so I modify the script downloaded from
> Dr.Bertini's website. The problem is that the
> structures generated by this script are identical.
This is probably due to the fact that the velocities are not randomized
before the high temperature dynamics. To randomize velocities, add the
lines
vector do (vx = maxwell($init_t)) (all)
vector do (vy = maxwell($init_t)) (all)
vector do (vz = maxwell($init_t)) (all)
before the first dynamics internal statement. Note also that IVM
topology is maintained between calls to dynamics internal, unless a
reset statement is specified.
best regards--
Charles
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.6 (GNU/Linux)
Comment: Processed by Mailcrypt 3.5.8+
iD8DBQFG0EZxPK2zrJwS/lYRAqWOAJwNljQ5Af3ZdPgUiyUvCNFKFarmqACfcWGK
ke8YBB/9/lq8gSdqJ6zq0Sw=
=GyDQ
-----END PGP SIGNATURE-----
---------------------------------
????????????????
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20070826/7b44a685/attachment.html
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: SpamAssassinReport.txt
Url:
http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20070826/7b44a685/attachment.txt
