It seems that in dist.RST the file (from which the distance restraint
information will be read) initial distance r2=115 on cluster and r2=15
on your computer. Check this please.
On Wed, Apr 6, 2011 at 6:15 PM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
> Dear Amber users,
>
> I came across a very strange problem when I performed SMD. I found the results obtained from the cluster and my own computer are completely different! I have read the manual and checked the mail-list, but the problem still cannot be solved. I even performed the example of smd simulation (/test/jar) on cluster and my computer respectively, I still found the same problem.
>
> Results from cluter:
> 115.00000 15.12396 998760.44518 0.00000
> 115.00500 15.09956 999054.42553 4994.53718
> 115.01000 15.07685 999331.52354 9990.50205
> 115.01500 15.05634 999586.55907 14987.79726
> 115.02000 15.03874 999812.55953 19986.29505
> 115.02500 15.02844 999965.59720 24985.74044
> 115.03000 15.02698 ************ 29985.72992
> 115.03500 15.03141 ************ 34985.89511
> 115.04000 15.04172 999982.77344 39985.94176
> 115.04500 15.05555 999894.54075 44985.63505
> 115.05000 15.07037 999796.33556 49984.86224
> 115.05500 15.08410 999708.99704 54983.62557
> 115.06000 15.09265 999673.47611 59982.08175
> 115.06500 15.09892 999660.79139 64980.41742
> 115.07000 15.09737 999726.26672 69978.88507
> 115.07500 15.09330 999816.95038 74977.74311
> 115.08000 15.08976 999902.41465 79977.04152
> 115.08500 15.08366 ************ 84976.83099
> 115.09000 15.07399 ************ 89977.26467
> 115.09500 15.06406 ************ 94978.43839
> 115.10000 15.06058 ************ 99980.19731
> 115.10500 15.06330 ************ 104982.22514
> 115.11000 15.07514 ************ 109984.13890
> 115.11500 15.09240 ************ 114985.57522
> 115.12000 15.11027 ************ 119986.38330
> 115.12500 15.12536 999996.43730 124986.61753
> 115.13000 15.13571 999942.87965 129986.46583
> 115.13500 15.14105 999939.48763 134986.17174
> 115.14000 15.13706 ************ 139986.09404
> 115.14500 15.12803 ************ 144986.59182
> 115.15000 15.10987 ************ 149988.01938
> 115.15500 15.09047 ************ 154990.63606
> 115.16000 15.07038 ************ 159994.48995
> 115.16500 15.04781 ************ 164999.66031
> 115.17000 15.03415 ************ 170005.98625
> 115.17500 15.02742 ************ 175013.07190
> 115.18000 15.03007 ************ 180020.50975
>
>
> Results from my computer:
> 15.00000 15.12396 -1239.55482 0.00000
> 15.00500 14.75768 2473.15435 3.08400
> 15.01000 15.13558 -1255.79414 6.12740
> 15.01500 15.14907 -1340.65261 -0.36372
> 15.02000 14.77035 2496.53852 2.52600
> 15.02500 15.12877 -1037.71408 6.17306
> 15.03000 15.17777 -1477.69021 -0.11545
> 15.03500 14.78810 2468.99680 2.36281
> 15.04000 15.12121 -812.13264 6.50497
> 15.04500 15.21140 -1663.95241 0.31476
> 15.05000 14.81200 2380.03972 2.10498
> 15.05500 15.11374 -587.42138 6.58653
> 15.06000 15.24212 -1821.18824 0.56500
> 15.06500 14.83812 2268.84550 1.68415
> 15.07000 15.10132 -313.17744 6.57332
> 15.07500 15.27260 -1976.02059 0.85032
> 15.08000 14.86053 2194.68405 1.39698
> 15.08500 15.09461 -96.12775 6.64337
> 15.09000 15.29175 -2017.47807 1.35935
> 15.09500 14.88712 2078.79152 1.51264
> 15.10000 15.09700 30.01635 6.78466
> 15.10500 15.31485 -2098.45710 1.61356\
> I am sure that all the input file are the same (I performed this simulation directly in the ./amber10/test/jar)!
> It seems that there are some problem with my cluster, but it works well for the MD.
> I am really sorry for bringing this trouble to you!
> Best wishes,
> Rilei Yu
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
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Received on Wed Apr 06 2011 - 07:30:04 PDT
