[gmx-users] Re: Simulation in the high temperature conditions

James Starlight jmsstarlight at gmail.com
Mon Apr 9 11:27:40 CEST 2012


> If you make your layer boundaries perpendicular to some axis then you can
> use position restraints on water oxygens that have non-zero force constants
> only with respect to that axis. Then relax the water position restraints
> before any others.
Yes, I've thought about this to apply posres onto selected coordinates to
allow waters move only laterally relavitely protein-membrane-like system.
But this prevent to move water into the receptor interious as well so it's
not very good aproach.

Also I've thought about vary of the ref_t oprions wich I've defined
separatelly for protein_membrane layer and for water_ions. As I've told I
want to increase confoprmation sampling of my protein by means of gradually
temperature increasing. Could I rise only ref_t for the protein_ccl4 layer
with the apllied posres on the protetn (backbone atoms) and ccl4 ( C atoms)
during nvt equilibration while not changing ref_t for water and ions ? Will
my system be some unphysicall in that case ?  Or as the alternative way
could I decrease ref_t for the water_ions layer in the end of nvt
equilibration to allow water to move out from the Ccl4 layer?

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120409/260e3b0a/attachment.html>

More information about the gromacs.org_gmx-users mailing list