Marcelo Fabricio Masman skrev:
Dear All.
Is there any tool (or set of tools) in GROMACS which allows me to
calculate #H2O vs time inside a pocket or in between two fragment of
a protein?
Any help and/or hint will be fully appreciated.
Marcelo
If you define an indexgroup for the pocket you could find the number of
water molecules within any given distance with g_bond -contact. Between
two protein fragments is a bit harder, because such a region is a bit
ill defined.
/Erik
--
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
_______________________________________________
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
