Thanks, Justin. Then does it mean I cannot use the program to do simulation
at this point? any suggestion on it?
Johnny
Date: Fri, 08 May 2009 12:31:31 -0400
From: "Justin A. Lemkul" <[email protected]>
Subject: Re: [gmx-users] Test-set
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Zhanglin Ni wrote:
The configurations are
Linux version 2.6.27.21-170.2.56.fc10.i686.PAE (gcc version 4.3.2
20081105 (Red Hat 4.3.2-7) (GCC) ) #1 SMP Mon Mar 23 23:24:26 EDT 2009
CPU1: Intel(R) Core(TM)2 Duo CPU E7400 @ 2.80GHz stepping 0a
lspci
00:00.0 Host bridge: Intel Corporation 82G33/G31/P35/P31 Express DRAM
Controller (rev 10)
00:02.0 VGA compatible controller: Intel Corporation 82G33/G31 Express
Integrated Graphics Controller (rev 10)
00:1b.0 Audio device: Intel Corporation 82801G (ICH7 Family) High
Definition Audio Controller (rev 01)
00:1d.0 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI
Controller #1 (rev 01)
00:1d.1 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI
Controller #2 (rev 01)
00:1d.2 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI
Controller #3 (rev 01)
00:1d.3 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI
Controller #4 (rev 01)
00:1d.7 USB Controller: Intel Corporation 82801G (ICH7 Family) USB2 EHCI
Controller (rev 01)
00:1e.0 PCI bridge: Intel Corporation 82801 PCI Bridge (rev e1)
00:1f.0 ISA bridge: Intel Corporation 82801GB/GR (ICH7 Family) LPC
Interface Bridge (rev 01)
00:1f.2 IDE interface: Intel Corporation 82801GB/GR/GH (ICH7 Family)
SATA IDE Controller (rev 01)
00:1f.3 SMBus: Intel Corporation 82801G (ICH7 Family) SMBus Controller
(rev 01)
01:08.0 Ethernet controller: Intel Corporation 82801G (ICH7 Family) LAN
Controller (rev 01)
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in tip4pflex
FAILED. Check files in water
The water test seems was the worse one. it showed like
....
Pressure (bar) step 50: 46893.3, step 50: 44603
Vir-XY step 50: -2423.21, step 50: -1880.2
Vir-XZ step 50: 667.327, step 50: 307.438
Vir-YX step 50: -2422.22, step 50: -1880.23
Vir-YY step 50: -3194.86, step 50: -2655.73
Vir-YZ step 50: -2208.7, step 50: -2608.7
Vir-ZX step 50: 667.878, step 50: 308.434
Vir-ZY step 50: -2207.77, step 50: -2608.41
Vir-ZZ step 50: -1482.41, step 50: -680.999
When I run the test set on my system (dual-core Intel MacBook), I get this
in
the tail end of the checkvir.out for water:
Pressure (bar) step 50: 46893.3, step 50: 45119.8
Vir-XX step 50: -6211.69, step 50: -6436.94
Vir-XY step 50: -2423.21, step 50: -1896.98
Vir-XZ step 50: 667.327, step 50: 316.873
Vir-YX step 50: -2422.22, step 50: -1896.65
Vir-YY step 50: -3194.86, step 50: -2648.67
Vir-YZ step 50: -2208.7, step 50: -2641.28
Vir-ZX step 50: 667.878, step 50: 318.282
Vir-ZY step 50: -2207.77, step 50: -2640.33
Vir-ZZ step 50: -1482.41, step 50: -817.011
It seems that your system is not producing the Vir-XX component, which may
be
what's causing the failure. The magnitude of difference between the other
energy terms is not substantially different from what I see (and my test
passes).
I now also recall you reported the following originally in your
checkpot.out:
There are 30 terms in the energy files
In my checkpot.out, the line reads:
There are 31 terms in the energy files
I suspect that is where the problem lies, but that is also where my
usefulness
ends. Perhaps one of the developers can comment at this point as to the
reason
for the missing energy term.
-Justin
Thanks
Johnny
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