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From: Jason Swails <jason.swails.gmail.com>

Date: Wed, 25 Apr 2012 18:23:54 -0400

On Wed, Apr 25, 2012 at 6:02 PM, Camille Sultana

<camillesultana.gmail.com>wrote:

*> So if I interpret this correctly, despite the fact that 1 and 4 are in the
*

*> excluded pair list, their interaction is not actually excluded in Amber's
*

*> calculations.
*

Correct -- this is an implementation detail that Tom alluded to. The main

non-bonded loop does NOT calculate any atoms in the exclusion list, which

means that atoms involved at two ends of a dihedral do not have their

nonbonded energies calculated in this subroutine.

In the subroutine that computes dihedral energies, 1-4 nonbonded

interactions are calculated *there*, and they are scaled by a given factor

(which is now given in the topology file).

*> Ok. Then my final question is how to interpret the energies
*

*> listed in the output file. For example if I had
*

*>
*

*> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 299.77 PRESS =
*

*> 0.0
*

*> Etot = 707.7731 EKtot = 641.5643 EPtot =
*

*> 66.2087
*

*> BOND = 72.1704 ANGLE = 267.0562 DIHED =
*

*> -67.7222
*

*> 1-4 NB = 230.9346 1-4 EEL = -1262.2843 VDWAALS =
*

*> -107.9538
*

*> EELEC = 934.0078 EHBOND = 0.0000 RESTRAINT =
*

*> 0.0000
*

*>
*

*> The overall question is have the 1-4 potentials listed already been added
*

*> to the results printed for eelec/vdw/dihed? If this is true listing the
*

*> 1-4 potentials independently is just to give extra information but they
*

*> have already been taken into account for the other potentials.
*

*>
*

The 1-4 potentials have NOT been added into EEL and VDW for 1-4 EEL and 1-4

VDW, respectively. They are calculated in separate subroutines and

accumulated independently.

You can verify this by adding up all of the energy terms, though, to be

sure. If the sum of every term is equal to the total sum reported, then

the 1-4s are not already added to VDW and EEL (this is what you should

get). If, however, you add up every term and you only get the reported

total energy by subtracting off the 1-4 terms, then you would know that

they've already been added into VDW and EEL (you should NOT get this).

HTH,

Jason

Quasi-related tangent:

As a side-note, this decomposition is helpful at times. For my own

example, MM/PBSA binding free energy analyses using a single trajectory

will have all internal potential terms cancel exactly (since the bound and

unbound conformations are identical). As a result, the 1-4 nonbonded

interactions should (and do) cancel out completely, which is a helpful

check for charge/VDW parameter consistency across different states.

Date: Wed, 25 Apr 2012 18:23:54 -0400

On Wed, Apr 25, 2012 at 6:02 PM, Camille Sultana

<camillesultana.gmail.com>wrote:

Correct -- this is an implementation detail that Tom alluded to. The main

non-bonded loop does NOT calculate any atoms in the exclusion list, which

means that atoms involved at two ends of a dihedral do not have their

nonbonded energies calculated in this subroutine.

In the subroutine that computes dihedral energies, 1-4 nonbonded

interactions are calculated *there*, and they are scaled by a given factor

(which is now given in the topology file).

The 1-4 potentials have NOT been added into EEL and VDW for 1-4 EEL and 1-4

VDW, respectively. They are calculated in separate subroutines and

accumulated independently.

You can verify this by adding up all of the energy terms, though, to be

sure. If the sum of every term is equal to the total sum reported, then

the 1-4s are not already added to VDW and EEL (this is what you should

get). If, however, you add up every term and you only get the reported

total energy by subtracting off the 1-4 terms, then you would know that

they've already been added into VDW and EEL (you should NOT get this).

HTH,

Jason

Quasi-related tangent:

As a side-note, this decomposition is helpful at times. For my own

example, MM/PBSA binding free energy analyses using a single trajectory

will have all internal potential terms cancel exactly (since the bound and

unbound conformations are identical). As a result, the 1-4 nonbonded

interactions should (and do) cancel out completely, which is a helpful

check for charge/VDW parameter consistency across different states.

-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Apr 25 2012 - 15:30:02 PDT

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