Dear All,
I would like to calculate a PMF for a reaction coordinates which involve forming bond between A-B, at the same time cleaving a bond between B-C.
I learnt from Bud that I may use "generalized distance coordinate restraint" to set the restraint and define the reaction coordinates. I lookup the manual. I found the restaint is defined as
U = k(w1|r1−r2|+w2|r3−r4|+w3|r5−r6|+w4|r7−r8|−r0)2
Is it same as the restrainst defined for LCOD?
I also want to reconfirm with you that if I should define the restraint files as follows, if I want to study the PMF when LCOD change from 1A to 10A?
# reaction coordinates
&rst iat(6)=A,B,B,C, r1=0., r2=1., r3=1., r4=10., rk2 = 30., rk3 = 30., /
Best regards,
Catherine
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Received on Wed Aug 11 2010 - 03:00:04 PDT
