Re: Is there solution to numerical inaccuracy

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Nov 26 2007 - 14:16:40 CST

Please also note that, apparently, charmm reads the random seed from the
restart files, whereas in namd you need to explicitly specify it to have
it be the same from run to run.
http://www.charmm.org/ubbthreads/showflat.php?Cat=0&Number=16096&Main=16053

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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