[AMBER] SMD negative distance

From: Jacopo Sgrignani <sgrigna.gmail.com>
Date: Mon, 10 Jan 2022 16:17:02 +0100

Dear All
we are performing SMD simulations to investigate the unbinding of a small
molecule from a transmembrane channel.

To 'force' the molecule to exit from the up and buttom side of the
membrane, we used this input:

 restraint between res4,5 - drug
&rst iat=-1,-1, fxyz=0,0,1, outxyz=1, r2=2, r2a=40, rk2=100,
igr1=9214,9219,9224,9230,9232 igr2=3397 /

the output is:

2.00000 -7.28347 18.56694 0.00000

It is not completely clear to me why the starting 'distance' is
negative... from the manual I understood it is a weighted distance but,
using iat=-1,-1, I'm not sure about what the program is printing.

Can you help me?


AMBER mailing list
Received on Mon Jan 10 2022 - 07:30:02 PST
Custom Search