AMBER Archive (2004)

Subject: AMBER: AMBER 6 compilation problems!

From: Grace Li (w24li_at_student.cs.uwaterloo.ca)
Date: Fri Jul 30 2004 - 12:17:39 CDT

Dear Amber Users:

I recently compiled AMBER 6 on my lab's cluster, I believe the cluster is
running in a unix based operating system with a intel pentium 4 processor
and g77 was used to compile the package.
I did a test Molecular Dynamics simulation of 1500 NSTEPs and compared it
to the output of the previous simulation that I did on a SGI
supercomputer. I noticed that after 900 NSTEPs the results starts to
differ as follows:

from my lab cluster>>>>>>>>>>
 NSTEP = 2350 TIME(PS) = 44.700 TEMP(K) = 313.16 PRESS = 0.00
 Etot = -3229.0084 EKtot = 787.8359 EPtot = -4016.8443
 BOND = 2.8060 ANGLE = 2.9679 DIHED = 3.1331
 1-4 NB = -0.1879 1-4 EEL = -261.5035 VDWAALS = 692.9282
 EELEC = -4456.9881 EHBOND = 0.0000 CONSTRAINT = 0.0000
 Ewald error estimate: 0.1298E-03

from the SGI machine >>>>>>>>>

NSTEP = 2350 TIME(PS) = 44.700 TEMP(K) = 306.94 PRESS = 0.00
 Etot = -3221.2988 EKtot = 772.1892 EPtot = -3993.4880
 BOND = 1.6549 ANGLE = 2.9067 DIHED = 3.3709
 1-4 NB = -0.1205 1-4 EEL = -261.1509 VDWAALS = 693.3475
 EELEC = -4433.4965 EHBOND = 0.0000 CONSTRAINT = 0.0000
 Ewald error estimate: 0.1634E-04

I was wondering if the differences in temperature here and and total
energy (Etot) is too big and if I have done something wrong with the
compilation?

Thanks for your help,

Grace
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