Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
I am trying to run a simulation of glucose in water using Gromacs
4.0.5 version. During equilibration gulcose was at the centre of the box
surrounded by water molecules. In the final results the gulcose come to
the one side of the box (behaviour like hydrophobic). I ploted rdf in
pure
water and glcose + water which is same.
Is there any bug in gromacs or I made some mistake or my results are
correct.
This is not a bug. It sounds more like your parameters for glucose are
too hydrophobic.
If the box is periodic, there is no "side" for a hydrophobic molecule to
prefer. Neither must it stay in the center. You can use trjconv to make
it look how you prefer.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
