AMBER Archive (2009)

Subject: [AMBER] Problem running test.pmemd.AMOEBA

From: mloureiro_at_cesga.es
Date: Fri Mar 13 2009 - 06:45:30 CDT

Hello,

I have installed AMBER10 and I have run the tests included.

I have a bit problem with tests that use AMOEBA.

-test.sander.AMOEBA --> all tests passed
-test.pmemd.AMOEBA --> all tests possible FAILURE
and if you check the file .out.dif you can see the differences are slight.

I have copied the beginnig of the file amoeba_wat1.out.dif to show the
problem.
Are right the results of test.pmemd.AMOEBA? Or maybe there is a problem with
the compilation stage? Should I worry about that?

35,36c35,36
< NATOM = 648 NTYPES = 1 NBONH = 1 MBONA = 1
< NTHETH = 1 MTHETA = 1 NPHIH = 1 MPHIA = 1 

---
>  NATOM  =     648 NTYPES =       1 NBONH =       0 MBONA  =       0
>  NTHETH =       0 MTHETA =       0 NPHIH =       0 MPHIA  =       0
38,39c38,39
<  NBONA  =       1 NTHETA =       1 NPHIA =       1 NUMBND =       1
<  NUMANG =       1 NPTRA  =       1 NATYP =       1 NPHB   =       1
---
>  NBONA  =       0 NTHETA =       0 NPHIA =       0 NUMBND =       0
>  NUMANG =       0 NPTRA  =       0 NATYP =       1 NPHB   =       0
56c56
<      ntf     =       8, ntb     =       1, igb     =       0, nsnb    =
   25
---
>      ntf     =       1, ntb     =       1, igb     =       0, nsnb    =
   25
-------------------------------------------------------------------------------->    3.  ATOMIC COORDINATES AND VELOCITIES
>
--------------------------------------------------------------------------------> water box
>  begin time read from input coords =     0. ps
88,89c87
< num_pairs_in_ee_cut,size_dipole_dipole_list =      39766     49707
<  NSTEP =        1   TIME(PS) =       0.001  TEMP(K) =   287.20  PRESS =
-1471.6
---
>  NSTEP =        1   TIME(PS) =       0.001  TEMP(K) =   287.20  PRESS = 
>     0.94d91
<  EKCMT  =         0.  VIRIAL  =         0.  VOLUME     =      6479.5881
97d93
<                                                     Density    =
0.9970
99c95
<  NSTEP =        2   TIME(PS) =       0.002  TEMP(K) =   291.07  PRESS =
-1466.8
---
>  NSTEP =        2   TIME(PS) =       0.002  TEMP(K) =   291.07  PRESS = 
>     0.104d99
<  EKCMT  =         0.  VIRIAL  =         0.  VOLUME     =      6479.5881
107d101
<                                                     Density    =
0.9970
109c103
<  NSTEP =        3   TIME(PS) =       0.003  TEMP(K) =   295.74  PRESS =
-128.2
---
>  NSTEP =        3   TIME(PS) =       0.003  TEMP(K) =   295.74  PRESS = 
>     0.114d107
<  EKCMT  =         0.  VIRIAL  =         0.  VOLUME     =      6479.5881
117d109
<                                                     Density    =
0.9970
119c111
<  NSTEP =        4   TIME(PS) =       0.004  TEMP(K) =   294.16  PRESS =
2130.7
---
>  NSTEP =        4   TIME(PS) =       0.004  TEMP(K) =   294.16  PRESS = 
>     0.124d115
<  EKCMT  =         0.  VIRIAL  =         0.  VOLUME     =      6479.5881
127d117
<                                                     Density    =
0.9970

Thanks,
Marta

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