VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Aug 05 2013 - 15:41:40 CDT

Surya,

from the ffTK documentation website:

  * Advanced Settings
     * Start, End, Delta: Control how the water molecule is moved with respect to the specified atom during the MM calculation.
     * Offset: Adjustment applied to distance of the water molecule at the QM energy minimum to account for differences between gas-phase and bulk-phase calculations.
     * Scale: Scaling factor applied to the QM minimum energy to account for the difference between gas-phase and bulk-phase calculations.

hence, the QM optimized position of the water, parsed from the QM target data, is shifted by the offset along the vector describing the interaction. ffTK then generates a trajectory of water molecule positions at a distance from the interaction site, in which the distance is specified relative to this shifted QM optimized position, over the range -0.4A < x < +0.4A in 0.05A increments. The MM interaction energy is computed at each of these positions for a given set of charges. The MMdistdelta which appears in the ffTK log file is the difference between the shifted QM position and where the minimum MM interaction energy is observed. it is critical that the MM interaction energy minimum if found WITHIN the scanned range, i.e., a true minimum is found. This can be assessed by visualizing the distance using COLP.

Regards,
Christopher Mayne

On Aug 5, 2013, at 12:06 PM, surya narayanan chandrasekaran wrote:

HI,
I have a doubt on the OPT_charge tab in FFTK

what is water shift setting start(-0.4) end (0.4) Delta(0.05) (is delta difference between? ) offset ?
is this water shift setting is return in MMdistdelta in log file?

thnkq 

--
Suryanarayanan C
M.S Chemist
01742857830