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?
thanks
jacopo
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Received on Mon Jan 10 2022 - 07:30:02 PST
