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

Date: Fri, 21 Nov 2008 19:12:44 -0500 (EST)

Dear Ross,

*> Note, however that I have seen many times where people try to fit their own
*

*> parameters and they produce a nice QM dihedral profile and then just fit the
*

*> dihedral term to this (forgetting all about including the 1-4 EEL and VDW
*

*> terms as well). Hence what they actually think they have fitted to they have
*

*> not and when they then include it in a large simulation they don't realize
*

*> that their actual force field parameters are bogus since they forgot the 1-4
*

*> contributions.
*

Thanks for your explanations, but I could not understand this paragraph

of yours. Let's say we have created a nice QM profile of a particular

torsion. To do the fitting, the MM energy without the dihedral energy of

this particular torsion should be calculated (let's call it MM_1). This

means that an frcmod file with zero torsional barrier of the particular

torsion needs to be used. Then, QM-MM_1 is calculated, which is fitted to

the desired cosine terms. If the fitting will include 2 cosine terms, for

example, QM-MM_1 should be fitted to V_1 * (1+cos(n1*x)) + V_2 *

(1+cos(n2*x)).

In the whole above process, the 1-4EEL and VDW terms are not

used/calculated explicitly. They are included in the MM_1

energy implicitly. Did you mean that? Thanks.

Best regards,

Date: Fri, 21 Nov 2008 19:12:44 -0500 (EST)

Dear Ross,

Thanks for your explanations, but I could not understand this paragraph

of yours. Let's say we have created a nice QM profile of a particular

torsion. To do the fitting, the MM energy without the dihedral energy of

this particular torsion should be calculated (let's call it MM_1). This

means that an frcmod file with zero torsional barrier of the particular

torsion needs to be used. Then, QM-MM_1 is calculated, which is fitted to

the desired cosine terms. If the fitting will include 2 cosine terms, for

example, QM-MM_1 should be fitted to V_1 * (1+cos(n1*x)) + V_2 *

(1+cos(n2*x)).

In the whole above process, the 1-4EEL and VDW terms are not

used/calculated explicitly. They are included in the MM_1

energy implicitly. Did you mean that? Thanks.

Best regards,

-- Ilyas Yildirim, Ph.D. --------------------------------------------------------------- = Hutchison Hall B#10 - Department of Chemistry = = - University of Rochester = = 585-275-6766 (office) - = = http://www.pas.rochester.edu/~yildirim/ = --------------------------------------------------------------- ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo.scripps.eduReceived on Fri Dec 05 2008 - 16:18:13 PST

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