Hi Christina,
Thank you so much for helping to spot my error. I mistakenly used
temp0=300.0 instead of 0.0 in the input file for the final quenched MD
step. Hopefully I will get more reasonable results after re-running
this final step. Thanks again!
Cheers,
Yaw Sing
On 9 November 2012 00:35, Christina Bergonzo <cbergonzo.gmail.com> wrote:
> 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 - 19:00:02 PST
