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

From: Thomas Steinbrecher <steinbrt.scripps.edu>

Date: Wed, 2 Apr 2008 10:31:57 -0700 (PDT)

Hi Aneesh,

If you are confused about the actual values for the LJ parameters written

into the topology file, they are computed like this:

in sander, the LJ equation is A/r^12 - B/r^6. In parm.dat, the parameters

correspond to this equation:

4 \eps [ 1/4 ( r0/r )^12 - 1/2 ( r0/r )^6 ]

where r0 is the energy minimum in a vdw pair. Another commonly seen form

of the LJ equation is:

4 \eps [ 1 / ( r/sigma )^12 - 1 / ( r/sigma )^6 ]

with sigma giving the zero crossing of the curve ( r0 = 2^(1/6) sigma ).

Every atom type contributes a given part to r0 which is given in the

forcefield.

An example where A and B come from for Cl:

in parm99.dat:

Cl 1.948 0.265

Therefore for two Cl r0 = 3.896 A (2 x 1.948), epsilon = 0.265 kcal/mol

in the prmtop, A and B are given then as:

ACOEFF 3.24E06 = epsilon * r0^12

BCOEFF 1.85E03 = 2 * epsilon * r0^6

The reason these parameters are given that way is it eases computation,

because A and B only need to be divided by the atom distance to get

E(vdw). The same obfuscation is done with the atomic partial charges.

This optimization is the reason why prmtop files are only

semi-humanreadable...

The reason for the zeros in the LJ fields is that many hydrogen atoms do

not have a LJ potential centered on them, therefore they contribute only

zeroes.

Regards,

Thomas

Dr. Thomas Steinbrecher

The Scripps Research Institute

10550 N. Torrey Pines Rd.

San Diego CA 92037, USA

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

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Fri Apr 18 2008 - 21:16:13 PDT

Date: Wed, 2 Apr 2008 10:31:57 -0700 (PDT)

Hi Aneesh,

If you are confused about the actual values for the LJ parameters written

into the topology file, they are computed like this:

in sander, the LJ equation is A/r^12 - B/r^6. In parm.dat, the parameters

correspond to this equation:

4 \eps [ 1/4 ( r0/r )^12 - 1/2 ( r0/r )^6 ]

where r0 is the energy minimum in a vdw pair. Another commonly seen form

of the LJ equation is:

4 \eps [ 1 / ( r/sigma )^12 - 1 / ( r/sigma )^6 ]

with sigma giving the zero crossing of the curve ( r0 = 2^(1/6) sigma ).

Every atom type contributes a given part to r0 which is given in the

forcefield.

An example where A and B come from for Cl:

in parm99.dat:

Cl 1.948 0.265

Therefore for two Cl r0 = 3.896 A (2 x 1.948), epsilon = 0.265 kcal/mol

in the prmtop, A and B are given then as:

ACOEFF 3.24E06 = epsilon * r0^12

BCOEFF 1.85E03 = 2 * epsilon * r0^6

The reason these parameters are given that way is it eases computation,

because A and B only need to be divided by the atom distance to get

E(vdw). The same obfuscation is done with the atomic partial charges.

This optimization is the reason why prmtop files are only

semi-humanreadable...

The reason for the zeros in the LJ fields is that many hydrogen atoms do

not have a LJ potential centered on them, therefore they contribute only

zeroes.

Regards,

Thomas

Dr. Thomas Steinbrecher

The Scripps Research Institute

10550 N. Torrey Pines Rd.

San Diego CA 92037, USA

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

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Fri Apr 18 2008 - 21:16:13 PDT

Custom Search