krithika krishnaswamy wrote:
hello,
Am a new user to gromacs.how to add water to a bilayer.i tried adding
water to entire system and then removed water from sides using tcl
script.But its not working.
Is there anyway to build lipid layer by layer and add water or something
can be done with genconf,genbox command so that water will not enter
middle region of bilayer.Please provide me with a detailed procedure.
There are several options listed on the wiki site:
http://wiki.gromacs.org/index.php/Membrane_Simulations
I find the genbox method to work quite well, myself. If you're getting water
from the "sides" of your bilayer, then your box vectors are wrong (i.e., too
large) for the system.
-Justin
-krithika
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
