Hi Yaw Sing,
I think what you're seeing here is the difference between well minimized
endpoints and intermediate structures at a higher temperature which have
just been annealed (temp = 300K, not zero) and where quenched MD has not
been performed yet. If you continue to cool to 0K and run quenched MD, you
should see the energies become more similar to the endpoint structure
energies. Alternatively, if you have run some simulations of the endpoints
at 300K, you can take a look and see what the potential energies are in
that simulation - they should be closer to the -105000 kcal/mol values you
see in the intermediate structures here. In either case, I would caution
you that for a large, explicitly solvated system potential energy along the
path is noisy at best, since the largest contribution to the potential
energy will come from solvent-solvent interactions.
Hope this helps,
Christina
On Thu, Nov 8, 2012 at 3:48 AM, Tan Yaw Sing <tanys.bii.a-star.edu.sg>wrote:
> Hi Amber users,
>
> I am performing nudged elastic band calculations on a protein system
> in explicit solvent. I noticed that the energies for the endpoints
> (shown below) are very far from the intermediate points at the end of
> my NEB run. I am using the same NEB parameters and protocol as the
> Amber tutorial A5, except for those relating to implicit solvent, and
> I am running the annealing step for slightly longer since my system is
> much bigger than the dipeptide in the tutorial.
>
> NSTEP = 100000 TIME(PS) = 920.000 TEMP(K) = 303.04 PRESS =
> 86.0
> Etot = -84034.0220 EKtot = 21396.2990 EPtot =
> -105430.3210
> BOND = 973.8880 ANGLE = 2603.0690 DIHED =
> 3338.0910
> 1-4 NB = 1121.9381 1-4 EEL = 9656.5119 VDWAALS =
> 11144.1954
> EELEC = -134268.0144 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> NEB replicate breakdown:
> Energy for replicate 1 = -149601.5096
> Energy for replicate 2 = -105224.9213
> Energy for replicate 3 = -105284.7919
> Energy for replicate 4 = -105322.5168
> Energy for replicate 5 = -105368.0022
> Energy for replicate 6 = -105706.5105
> Energy for replicate 7 = -105285.5549
> Energy for replicate 8 = -105215.8000
> Energy for replicate 9 = -105175.5311
> Energy for replicate 10 = -105407.6115
> Energy for replicate 11 = -105404.0531
> Energy for replicate 12 = -105189.3027
> Energy for replicate 13 = -105329.3757
> Energy for replicate 14 = -105476.4810
> Energy for replicate 15 = -105281.1999
> Energy for replicate 16 = -105475.2188
> Energy for replicate 17 = -105476.2020
> Energy for replicate 18 = -105321.5064
> Energy for replicate 19 = -105077.3354
> Energy for replicate 20 = -105388.9111
> Energy for replicate 21 = -105456.9010
> Energy for replicate 22 = -105234.7272
> Energy for replicate 23 = -105358.6921
> Energy for replicate 24 = -105423.5303
> Energy for replicate 25 = -105446.2198
> Energy for replicate 26 = -105189.0672
> Energy for replicate 27 = -105585.0960
> Energy for replicate 28 = -105197.3642
> Energy for replicate 29 = -105354.3470
> Energy for replicate 30 = -105188.3794
> Energy for replicate 31 = -105430.3210
> Energy for replicate 32 = -149554.4709
> Total Energy of replicates = -3459431.4522
> EKCMT = 8802.7356 VIRIAL = 8169.0047 VOLUME =
> 341491.8761
> Density =
> 1.0291
> Ewald error estimate: 0.7207E-04
>
> Has anyone encountered this "problem" when using explicit solvent for
> NEB calculations? Or is this normal for explicit solvent systems? I
> have started a trial run using implicit solvent with the same protocol
> and the distribution of the energies among the replicates look
> reasonable. Would gladly appreciate some help with this. Thanks.
>
> -Yaw Sing
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
----------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Fellow
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Office: Biopolymers Room 295
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Nov 08 2012 - 09:00:03 PST
