Dear Amber users,
I am facing a peculiar problem in running AMBER (Amber12 and AmberTools13).
I have complied AMBER on 21/05/2014 in a machine having 64 bit Ubuntu 12.04
LTS (server edition) with AMD opteron 6200 (16 core). During the NVT
equilibration process *(tem0=300.0K)* in explicit solvent the temp. reaches
to ~4000.0K and it stays tiil the NSLIM.
*Output*
------------------------------------------------------------------------------
NSTEP = 5000 TIME(PS) = 10.000 *TEMP(K) = 3908.32* PRESS =
0.0
Etot = 90471.3668 EKtot = 89960.2013 EPtot =
511.1655
BOND = 674.8848 ANGLE = 1395.6137 DIHED =
718.0662
1-4 NB = 243.6672 1-4 EEL = -394.4273 VDWAALS =
8058.9215
EELEC = -11037.0200 EHBOND = 0.0000 RESTRAINT =
851.4594
EAMBER (non-restraint) = -340.2939
Ewald error estimate: 0.1491E+00
------------------------------------------------------------------------------
Whereas when I recompiled the same AMBER on the same date in another
machine having 64bit Ubuntu 12.04 LTS (Desktop version) with Intel Xeon
E5-2609 (8 core), the same simulation (as mentioned above) goes fine, where
it satisfies the *temp0*.
*Output*
------------------------------------------------------------------------------
NSTEP = 5000 TIME(PS) = 10.000 *TEMP(K) = 302.91* PRESS =
0.0
Etot = -30535.4721 EKtot = 6972.1931 EPtot =
-37507.6652
BOND = 163.7116 ANGLE = 320.7394 DIHED =
466.8314
1-4 NB = 163.3470 1-4 EEL = -363.6741 VDWAALS =
4497.9322
EELEC = -42858.9286 EHBOND = 0.0000 RESTRAINT =
102.3757
EAMBER (non-restraint) = -37610.0410
Ewald error estimate: 0.5023E-04
------------------------------------------------------------------------------
Kindly suggest what could be the reason for this and what should be done in
this case if I am also willing to use the first machine (having AMD
opteron)?
Looking forward for your reply.
---------------------------------------------------------------------
Indrajit Deb
Kolkata, India.
Mob: +919239202278
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Received on Wed May 21 2014 - 07:00:03 PDT
