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From: Andrey Frolov <frolov.mis.mpg.de>

Date: Thu, 01 Jul 2010 18:16:38 +0200

Dear NAB and 3D-RISM Developers,

I would like to run some simulation in NAB of AmberTools with 3D-RISM

and i have some questions (in addition to my previous message):

1.

What is the "tolerance" statement (like:

mm_options("tolerance=1e-11");)? In manual it is written that this is

residual, but how actually it is calculated: is it a L2 norm for the 3D

total correlation functions h (or maybe c or gamma):

tolerance = (\sum_{number of 3D functions} [ \int_{V} (h_new -

h_old) dV ] ) / {number of 3D functions}

where h_new and h_old - 3D arrays functions of two subsequent

iterations.?

2.

If i gave a right definition of the "tolerance", why the proposed value

for minimization (and i suppose for one point calculation) with

3D-RISM is so small 10-11? I suppose that the accuracy 10-5 is more

the enough if we want to calculate chemical potential out of total

correlation functions.

Are there some obstacles that i do not see so far?

And what is an appropriate value of "tolerance" to use for 1 point

calculation of chemical potential without wasting too much of computer

resources?

I would be very pleased if you know something about the questions and

drop me a message.

Thank you very much.

Andrey Frolov, PhD student at Max Planck Institute for Mathematics in

the Sciences, Germany

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Jul 01 2010 - 09:30:05 PDT

Date: Thu, 01 Jul 2010 18:16:38 +0200

Dear NAB and 3D-RISM Developers,

I would like to run some simulation in NAB of AmberTools with 3D-RISM

and i have some questions (in addition to my previous message):

1.

What is the "tolerance" statement (like:

mm_options("tolerance=1e-11");)? In manual it is written that this is

residual, but how actually it is calculated: is it a L2 norm for the 3D

total correlation functions h (or maybe c or gamma):

tolerance = (\sum_{number of 3D functions} [ \int_{V} (h_new -

h_old) dV ] ) / {number of 3D functions}

where h_new and h_old - 3D arrays functions of two subsequent

iterations.?

2.

If i gave a right definition of the "tolerance", why the proposed value

for minimization (and i suppose for one point calculation) with

3D-RISM is so small 10-11? I suppose that the accuracy 10-5 is more

the enough if we want to calculate chemical potential out of total

correlation functions.

Are there some obstacles that i do not see so far?

And what is an appropriate value of "tolerance" to use for 1 point

calculation of chemical potential without wasting too much of computer

resources?

I would be very pleased if you know something about the questions and

drop me a message.

Thank you very much.

Andrey Frolov, PhD student at Max Planck Institute for Mathematics in

the Sciences, Germany

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Jul 01 2010 - 09:30:05 PDT

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