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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>
--
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
