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From: Ilyas Yildirim <yildirim.pas.rochester.edu>

Date: Thu, 3 Mar 2005 19:24:03 -0500 (EST)

Dear David Case,

In my prev. emails, I was asking why AMBER does not let us use dummy

atoms in the initial state when k is not equal to 1 (pp.134, note #2). And

as far as I understand, the reason lies at the parameter function chosen

in Eq. # 5 (pp.133). When I plot the function, (1-lambda)^k, it seems

that when we have dummy atoms at the initial state, the transformation

will be sharp. It is not as gradual as it is when we have dummy atoms at

the final state.

So, we were thinking that if we use a parameter function,

tanh[k(2lambda-1)], such that the Eq. 5 becomes,

V(lambda)= tanh[k(2lambda-1)]*V0 + {1 - tanh[k(2lambda-1)]}*V1

the problem might be solved. When we plot the function tanh[k(2lambda-1)],

we see that the initial and the final transformations look gradual. So, we

were wondering how we can change the AMBER code such that we can use this

new function rather the old one. Do we have to change just the

thermo_int.f file, or something else too? Thanks in advance.

Best regards,

Date: Thu, 3 Mar 2005 19:24:03 -0500 (EST)

Dear David Case,

In my prev. emails, I was asking why AMBER does not let us use dummy

atoms in the initial state when k is not equal to 1 (pp.134, note #2). And

as far as I understand, the reason lies at the parameter function chosen

in Eq. # 5 (pp.133). When I plot the function, (1-lambda)^k, it seems

that when we have dummy atoms at the initial state, the transformation

will be sharp. It is not as gradual as it is when we have dummy atoms at

the final state.

So, we were thinking that if we use a parameter function,

tanh[k(2lambda-1)], such that the Eq. 5 becomes,

V(lambda)= tanh[k(2lambda-1)]*V0 + {1 - tanh[k(2lambda-1)]}*V1

the problem might be solved. When we plot the function tanh[k(2lambda-1)],

we see that the initial and the final transformations look gradual. So, we

were wondering how we can change the AMBER code such that we can use this

new function rather the old one. Do we have to change just the

thermo_int.f file, or something else too? Thanks in advance.

Best regards,

-- Ilyas Yildirim --------------------------------------------------------------- - Department of Chemisty - - - University of Rochester - - - Hutchison Hall, # B10 - - - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) - - http://www.pas.rochester.edu/~yildirim/ - --------------------------------------------------------------- ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Fri Mar 04 2005 - 00:53:00 PST

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