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From: Marek Maly <marek.maly.ujep.cz>

Date: Fri, 09 Dec 2011 19:44:21 +0100

Hi Thomas,

thanks for the prompt reply !

I agree that if the software should manage all possible (arbitrarily

complicated) TI

transformations the most general formula for V(L) has to be implemented in

source codes.

It was just a little hard for me to realize (from this general formula)

how it exactly works during the simulation.

In another words which steps are done in the given MD run in given L value

in the given time ti.

My actual interpretation of the implementation of general formula

V(L) = (1-L) V0 + L V1

is that during the MD run with the given L value in the given time step ti

a) the atom interactions (potentials, forces) are calculated according to

potential V0, using the actual coordinates

b) the atom interactions (potentials, forces) are calculated according to

potential V1, using the actual coordinates

c) the final atom interactions (potential energy, final forces necessary

to propagate the system in time) are calculated

as the L-linear combination of those calculated in a) and b).

Then also dV/dL is calculated (here simple as V1-V0).

I hope that I finally got it :)) if not I have probably to try study

sander source codes and

try more often some gym to promote blood circulation in my brain :))

Anyway thanks again for your help !

Best wishes,

Marek

I thing that for all technical details the best way is really to check

relevant source files.

Dne Fri, 09 Dec 2011 09:53:00 +0100 <steinbrt.rci.rutgers.edu> napsal/-a:

*> Hi all,
*

*>
*

*>> The both interpretations gives the same expression for the total
*

*>> lambda-dependend el. energy and it's lambda derivative
*

*>> (so there is really just difference in V interpretation). But after all
*

*>> I
*

*>
*

*> that is true in your example, but assume a more complicated case: A and B
*

*> are connected by a bond the length of which changes from V0 to V1, plus
*

*> qa
*

*> and qb change as well. Then it becomes easier to write:
*

*>
*

*> V(l) = (1-l) V0 * l V1
*

*>
*

*> and compute V0 and V1 by one sander process each. That certainly isn't
*

*> the
*

*> only possible way to do it but that's how it is in sander at the moment.
*

*>
*

*> Kind Regards,
*

*>
*

*> Thomas
*

*>
*

*> Dr. Thomas Steinbrecher
*

*> formerly at the
*

*> BioMaps Institute
*

*> Rutgers University
*

*> 610 Taylor Rd.
*

*> Piscataway, NJ 08854
*

*>
*

*> __________ Informace od ESET NOD32 Antivirus, verze databaze 6695
*

*> (20111208) __________
*

*>
*

*> Tuto zpravu proveril ESET NOD32 Antivirus.
*

*>
*

*> http://www.eset.cz
*

*>
*

*>
*

*>
*

Date: Fri, 09 Dec 2011 19:44:21 +0100

Hi Thomas,

thanks for the prompt reply !

I agree that if the software should manage all possible (arbitrarily

complicated) TI

transformations the most general formula for V(L) has to be implemented in

source codes.

It was just a little hard for me to realize (from this general formula)

how it exactly works during the simulation.

In another words which steps are done in the given MD run in given L value

in the given time ti.

My actual interpretation of the implementation of general formula

V(L) = (1-L) V0 + L V1

is that during the MD run with the given L value in the given time step ti

a) the atom interactions (potentials, forces) are calculated according to

potential V0, using the actual coordinates

b) the atom interactions (potentials, forces) are calculated according to

potential V1, using the actual coordinates

c) the final atom interactions (potential energy, final forces necessary

to propagate the system in time) are calculated

as the L-linear combination of those calculated in a) and b).

Then also dV/dL is calculated (here simple as V1-V0).

I hope that I finally got it :)) if not I have probably to try study

sander source codes and

try more often some gym to promote blood circulation in my brain :))

Anyway thanks again for your help !

Best wishes,

Marek

I thing that for all technical details the best way is really to check

relevant source files.

Dne Fri, 09 Dec 2011 09:53:00 +0100 <steinbrt.rci.rutgers.edu> napsal/-a:

-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Dec 09 2011 - 11:00:02 PST

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