Dear Amber Users,
Yes my system is small with around 200 atoms .
I have another question , when I solvate my previous systems with TIP3PBOX
.My minimization output file shows up as below with negative energy profile
. I would like to know the reason for this .Is it related to electrostatics
of the system .:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -5.3765E+03 1.1957E+01 1.1780E+02 C3 54
BOND = 83.3722 ANGLE = 111.4176 DIHED =
11.0838
VDWAALS = 709.4663 EEL = -6306.5299 HBOND =
0.0000
1-4 VDW = 13.6059 1-4 EEL = 1.1321 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -6.8055E+03 2.8127E+00 7.1710E+01 C2 53
BOND = 401.9747 ANGLE = 82.6036 DIHED =
16.6673
VDWAALS = 720.8712 EEL = -8040.9193 HBOND =
0.0000
1-4 VDW = 12.0920 1-4 EEL = 1.2157 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -7.1563E+03 9.3186E-01 5.3313E+00 C2 53
BOND = 431.8288 ANGLE = 78.8985 DIHED =
17.4077
VDWAALS = 826.8493 EEL = -8524.4105 HBOND =
0.0000
1-4 VDW = 11.7925 1-4 EEL = 1.2895 RESTRAINT =
0.0000
Your help is highly appreciated .
Thanks
John.
On Tue, Mar 2, 2010 at 12:24 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
>
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Received on Tue Mar 02 2010 - 11:00:03 PST
