Re: [AMBER] Problem on SMD

From: Dmitry Nilov <nilovdm.gmail.com>
Date: Wed, 6 Apr 2011 18:28:52 +0400

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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 06 2011 - 07:30:04 PDT
Custom Search