Dear amber users,
I am doing SGMD (self guided molecular dynamics) with
Amber 9.0 version. But the simulation get terminated with some error as
shown below after 6ns run.
******************************************************************************************
MPI Application rank 11 exited before MPI_Finalize() with status 1
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line
Source
libpthread.so.0 0000003CE890C4F0 Unknown Unknown Unknown
libmpi.so.1 0000002A956EBDDD Unknown Unknown Unknown
libmpi.so.1 0000002A956D7165 Unknown Unknown Unknown
libmpi.so.1 0000002A957437DA Unknown Unknown Unknown
libmpi.so.1 0000002A95733C88 Unknown Unknown Unknown
libmpi.so.1 0000002A95749F20 Unknown Unknown Unknown
sander.MPI 00000000004ED9AF Unknown Unknown Unknown
sander.MPI 00000000004BD5D4 Unknown Unknown Unknown
sander.MPI 00000000004B2FAD Unknown Unknown Unknown
sander.MPI 0000000000404DA2 Unknown Unknown Unknown
libc.so.6 0000003CE821C3FB Unknown Unknown Unknown
sander.MPI 0000000000404CEA Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
**********************************************************************************************
Here is input for SGMD.........
********************************************************
&cntrl
imin = 0, ntx = 7, irest = 1,
ntpr = 100, ntwx = 500, ntwe = 0,
ntc = 2, ntf = 2,iwrap = 0,
nstlim = 1000000, dt =0.002,
tempi=274.0, temp0 = 274.0, ntt =1, tautp =1.0,
ntb = 1, ntp = 0,cut =12.0,
isgld =1, tsgavg =0.2, tempsg =1.0,
isgsta =8701, isgend =8826 ( atom numbers of protein)
&end
**********************************************************
and at the end of the run the output file look like as
shown.................
***************************************************************************************************
NSTEP = 233800 TIME(PS) = 6767.600 TEMP(K) = 289.61 PRESS =
0.0
Etot = -11218.2624 EKtot = 7343.7475 EPtot =
-18562.0099
BOND = 2779.1812 ANGLE = 3562.7218 DIHED =
4418.6891
1-4 NB = 1301.6957 1-4 EEL = 26368.3968 VDWAALS =
-4423.1948
EELEC = -52569.4997 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.1366E-04
SGFT= 0.8172 TEMPSGI= 1.0000 K
------------------------------------------------------------------------------
NSTEP = 233900 TIME(PS) = 6767.800 TEMP(K) = 284.05 PRESS =
0.0
Etot = -11117.5166 EKtot = 7202.8946 EPtot =
-18320.4112
BOND = 2829.0841 ANGLE = 3809.7204 DIHED =
4370.6374
1-4 NB = 1333.1363 1-4 EEL = 26341.0330 VDWAALS =
-4377.1936
EELEC = -52626.8286 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.5218E-04
SGFT= 0.6368 TEMPSGI= 1.0000 K
------------------------------------------------------------------------------
*************************************************************************************************************
what could be the reason for this early termination? Waiting for your
valuable reply....
Thanks in advance
Sincerely
Aneesh
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Received on Mon Mar 22 2010 - 23:30:03 PDT
