From: Alok Juneja (juneja_at_speakeasy.net)
Date: Mon Nov 26 2007 - 04:54:22 CST
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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