ABF

From: karthik kumar (karthik3327_at_gmail.com)
Date: Mon Apr 15 2013 - 07:38:26 CDT

• Next message: Magnus Andersson: "restrain ligand to z-interval"
• Previous message: Magnus Andersson: "restrain ligand in z-interval"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi USERS,

I am running ABF calculations for studying the dimerization free energy
profile in bulk solution.

Initially, two molecules are separated by distance of 3 A centered in box
of size 55A.

I have defined reaction coordinate to evolve from 2A to 15 A.

At some point two molecules moves to edge of the box and their comes the
actual problem. (RC is not PBC & RC is suddenly increasing to around 25A)

I can fix the first molecule center of mass to overcome this problem . will
that wont effect FE profile?

orelse is there any better solution to overcome this PBC issue.

Thanks a lot in advance

Karteek Kumar

• Next message: Magnus Andersson: "restrain ligand to z-interval"
• Previous message: Magnus Andersson: "restrain ligand in z-interval"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:09 CST