Hello,
On Mon, Mar 1, 2010 at 11:50 PM, John S <s.john634.gmail.com> wrote:
> Dear Amber Users ,
>
> While carrying out energy minimization using non periodic boundary
> conditions using igb=1 .
> Even after going through steepest descent minimization , my system shows a
> high energy .Is it normal to get this in cyclic compounds .
Single point energies are not nearly as informative as energy
differences, especially considering the fact that the "zero" energy is
completely arbitrary for a force field. It appears as though your
system is rather small, and your energy is ~68.3 kcal/mol. This does
not seem terribly high...
When you are performing a minimization, the factors you want to look
at the closest are the RMS and the gradient. These will tell you how
stressed your system is (i.e. how far from a minimum it is).
Considering the fact that these values are very small, I'd say your
system is near a minimum (which is probably not surprising considering
how small the system appears to be).
Also note that the bonded terms must necessarily be positive based on
how the amber force field is defined. Indeed, contribution for each
of these terms is 0 in their equilibrium position. Only VDW and
electrostatics (including the 1-4 interactions and solvation terms for
implicit solvent) can be negative, as some of them are.
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1800 6.8299E+01 3.0163E-03 1.7630E-02 C2 53
>
> BOND = 3.8707 ANGLE = 44.7856 DIHED =
> 8.7678
> VDWAALS = -1.7451 EEL = 0.5667 EGB =
> -1.7387
> 1-4 VDW = 12.2132 1-4 EEL = 1.5783 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1900 6.8299E+01 2.4809E-03 1.1919E-02 C2 53
>
> BOND = 3.8704 ANGLE = 44.7861 DIHED =
> 8.7674
> VDWAALS = -1.7450 EEL = 0.5667 EGB =
> -1.7387
> 1-4 VDW = 12.2132 1-4 EEL = 1.5783 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2000 6.8299E+01 1.5407E-03 6.8580E-03 C2 28
>
> BOND = 3.8706 ANGLE = 44.7863 DIHED =
> 8.7669
> VDWAALS = -1.7449 EEL = 0.5667 EGB =
> -1.7387
> 1-4 VDW = 12.2132 1-4 EEL = 1.5783 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2100 6.8298E+01 1.0520E-03 3.1501E-03 H16 26
>
> BOND = 3.8707 ANGLE = 44.7866 DIHED =
> 8.7665
> VDWAALS = -1.7448 EEL = 0.5667 EGB =
> -1.7387
> 1-4 VDW = 12.2132 1-4 EEL = 1.5783 RESTRAINT =
> 0.0000
>
All the best,
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 01 2010 - 21:30:04 PST
