- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Thomas Huber <Thomas_Huber_at_Physik.TU-Muenchen.DE>

Date: Tue 10 Apr 2001 22:02:43 +0200 (MET DST)

Hi Artem,

if you compare different papers about vdW radii, then you have to look for

the particular definition of the radius. Sometimes they are defined as the

half of the distance between identical atoms at minimum interaction

energy, and as I recall (unfortunately I don't have the time to look it

up) as the half of the distance at zero (!) interaction energy, which

would correspond to the hard spere radius.

Regardless of the actual definition, each paper should describe the

analytical term to calculate the interaction energy, so if you have a

parameter set and an equation, just fill in the values into the formula

and compare it with the other paper. After some rearrangements, you'll

probably find the parameters of being equivalent.

Thomas

-----------------------------------------------------------------------------

Dr.Thomas Huber University of Arizona

Tel.: (520) 621-2537 Department of Chemistry

FAX: (520) 621-8407 1306 E. University Blvd.

email thuber_at_physik.tu-muenchen.de Tucson, Arizona 85721-0041

On Tue, 10 Apr 2001, artem wrote:

*> Dear Amber users,
*

*>
*

*> I've noticed that Van der Waals radius for TIP3P in Amber (parm94.dat)
*

*> is different from original TIP3P model reported in J. Chem. Phys., 1983,
*

*> 79, 926-935. Amber has 1.7683 angs and the original has 1.5753 angs. I
*

*> can assume that Amber's radius comes from some additional
*

*> parametrisation. Does anybody have references about the justificationof
*

*> Amber's TIP3P Van der Waals radius? What radius should i use if i wantto
*

*> switch on SPC model?
*

*>
*

*> thanks a lot
*

*>
*

*> Artem Mamonov
*

*> Chemistry Department
*

*> University of Pittsburgh
*

*>
*

*>
*

Received on Tue Apr 10 2001 - 13:02:43 PDT

Date: Tue 10 Apr 2001 22:02:43 +0200 (MET DST)

Hi Artem,

if you compare different papers about vdW radii, then you have to look for

the particular definition of the radius. Sometimes they are defined as the

half of the distance between identical atoms at minimum interaction

energy, and as I recall (unfortunately I don't have the time to look it

up) as the half of the distance at zero (!) interaction energy, which

would correspond to the hard spere radius.

Regardless of the actual definition, each paper should describe the

analytical term to calculate the interaction energy, so if you have a

parameter set and an equation, just fill in the values into the formula

and compare it with the other paper. After some rearrangements, you'll

probably find the parameters of being equivalent.

Thomas

-----------------------------------------------------------------------------

Dr.Thomas Huber University of Arizona

Tel.: (520) 621-2537 Department of Chemistry

FAX: (520) 621-8407 1306 E. University Blvd.

email thuber_at_physik.tu-muenchen.de Tucson, Arizona 85721-0041

On Tue, 10 Apr 2001, artem wrote:

Received on Tue Apr 10 2001 - 13:02:43 PDT

Custom Search