From: Alok Juneja (juneja_at_speakeasy.net)
Date: Thu Nov 29 2007 - 12:04:50 CST
Dear Peter,
Yes, I am specifying the identical seed value in A (complete run), B1
(1st half) and B2 (2nd half). A is one complete run where as B1 & B2
simulations are serial that means that I am using the restart file of B1
for the B2 run.
Peter, I am not clear with what do you mean by serial or parallel? As I
mentioned earlier my runs BI and B2 are serial. This simulation I am
running on single same processor. Kindly mention the link where the
non-determinism of the Langevin thermostat in parallel has been talked
about.
So comming back to square one, after reading all the comments in this
discussion, I believe there exist NO solution to this problem that is
occuring either because of numerical inaccuracy or non-determinism.
Could the B1 and B2 MD runs be considered as good as single A MD run.
-Alok
Peter Freddolino wrote:
>Hi Alok,
>just to verify, since you're running NVT, did you specify a seed value
>in your config file for the A-B1-B2 simulations? And were your
>production runs serial or parallel? If your production runs are done in
>parallel then the differences you observe in the first part of your
>email are really unremarkable, and have nothing to do with precision and
>everything to do with the nondeterminism of the langevin thermostat in
>parallel that has been mentioned earlier.
>Best,
>Peter
>
>Alok Juneja wrote:
>
>
>>Dear Peter, Dave, Himanshu & other list member,
>>
>>Sorry for not answering ealier though I was regularly following the
>>discussion on this issue. As requested by Peter, I am providing my
>>findings about this issue..
>>
>>I am running constant temperature 50 ns dynamics, total of 25000000
>>steps with time step of 0.002ps and dcdfreq of 100 however restartfreq
>>of 100000. Somehow my MD crashed at 5459300 but my last restrart was
>>5400000. I restarted with this. I am doing this MD to see the protein
>>behavious and am calculating the N and C terminal distance (Ang.).
>>Following is the N-C terminal distance before crash and after crash. I
>>am running this simulation in parallel.
>>
>># TIME(PS) Before-Crash After-Crash
>>10800 10.833
>>10800.2 11.3259 11.0924
>>10800.4 11.2417 11.1039
>>10800.6 10.985 10.9962
>>10800.8 10.7715 11.1593
>>10801 11.3783 11.4828
>>10801.2 11.1862 10.9861
>>10801.4 11.3925 10.9671
>>10801.6 10.8473 10.9287
>>(*) 10801.8 10.5789 11.013
>>10802 10.8792 10.4324
>>10802.2 10.6182 10.4422
>>10802.4 10.8918 10.6541
>>10802.6 10.9267 10.7829
>>10802.8 10.6352 10.8386
>>10803 10.8069 10.4295
>>(*) 10803.2 11.3242 10.5952 (*) 10803.4
>>11.3397 10.4784
>>(*) 10803.6 11.5822 10.4696
>>(*) 10803.8 11.023 10.8231
>>10804 10.9887 10.4586
>>10804.2 10.5118 10.3266
>>(*) 10804.4 10.4329 9.95989
>>10804.6 10.6863 10.2366
>>(*) 10804.8 11.3551 10.2149
>>(*) 10805 11.3445 9.88589
>>10805.2 10.7702 10.1757
>>10805.4 10.4436 10.3636
>>10805.6 10.3206 10.2086
>>10805.8 10.8214 10.5937
>>10806 11.2742 10.3849
>>10806.2 11.44 10.2721
>>(*) 10806.4 11.2566 10.1909
>>10806.6 10.9381 10.7606
>>10806.8 11.5617 10.8286
>>10807 11.7283 11.246
>>10807.2 11.4038 11.2901
>>10807.4 10.5862 10.708
>>10807.6 10.61 10.6308
>>10807.8 11.1818 10.2391
>>10808 11.3433 10.5278
>>10808.2 11.1947 11.0142
>>10808.4 10.9988 11.2578
>>(*) 10808.6 10.447 11.334
>>10808.8 10.3205 10.9368
>>10809 10.7634 10.9165
>>10809.2 10.7874 11.1041
>>10809.4 11.011 11.15
>>10809.6 10.8222 10.9214
>>10809.8 10.8731 10.2806
>>10810 11.0003 10.908
>>
>>You will find so many time steps where the difference is remarkable
>>(indicated by *). I believe that these difference is too much for me.
>>I checked this and found that this is not the case with CHARMM where
>>you get the identical results even after restart.
>>
>>For your ready reference, I am attaching the total energy graph for
>>comparision (comparision.pdf
>>[http://www.geocities.com/junejaalok/comparision.pdf]).
>>As requested by Dave, I am attaching file A-B1-B2.pdf
>>[http://www.geocities.com/junejaalok/A-B1-B2.pdf], the job run on
>>single same processor.
>>
>>Test A energy profile on [http://www.geocities.com/junejaalok/testA.txt]
>>TestB1 energy profile on [http://www.geocities.com/junejaalok/testB1.txt]
>>TestB2 energy profile on [http://www.geocities.com/junejaalok/testB2.txt]
>>
>>since, i am restricted the with the amount of characters that one can
>>write in NAMD forum and the size of attachments, I am putting an extra
>>links for you to see the files and results..hope you understand.
>>
>>I appreciate your efforts to get into the depth. But I believe the
>>NAMD developers should really think over this issue..however, any
>>solution and suggestions in this regard would be of great help for
>>others as well..
>>
>>
>>Best Wishes,
>>Alok
>>
>>
>
>
>
>
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