Why do different versions of NAMD deserve different simulation results?

From: ع (he.yuhui.ime_at_gmail.com)
Date: Mon Dec 20 2010 - 06:03:03 CST

Dear all,

    I am now doing some NAMD simulation of nanopore-based DNA
translocation. At first, I ran NAMD_2.7b4_Linux-x86 version, which is a
32-bit version on my laptop. What I found was that during the energy
minimization stage, the vdW energy is always unreasonable:

[helios_at_RedHat-He Nanopore]$ tail -10 eq0.log
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 90 118865.4983 7383.7350 0.0000
0.0000 -2539917.9652 9999999999.9999 0.0000
0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999
9999999999.9999 0.0000 9999999999.9999 9999999999.9999
1208309.6819 9999999999.9999 9999999999.9999

WRITING COORDINATES TO DCD FILE AT STEP 90
ENERGY: 91 118727.1852 7458.6476 0.0000
0.0000 -2540168.0669 9999999999.9999 0.0000
0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999
9999999999.9999 0.0000 9999999999.9999 9999999999.9999
1208309.6819 9999999999.9999 9999999999.9999

WRITING COORDINATES TO DCD FILE AT STEP 91

     At first, I thought there might be some atoms which were too close to
each other, leading to extreme values of vdW energy. However, I checked the
PDB file by writing some VMD codes, and found no such case.

     The more incredible finding is that when I run the same namd script
with the same PDB and PSF file on the workstation, where
NAMD_2.7b1_Linux_x86_64 is installed, the above artifact never happens!

LDB: ============== END OF LOAD BALANCING =============== 518.576

Info: Initial time: 1 CPUs 5.16644 s/step 59.7968 days/ns 148.165 MB memory
TIMING: 100 CPU: 514.58, 5.0948/step Wall: 521.851, 5.16675/step, 0 hours
remaining, 148.165436 MB of memory in use.
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 100 143463.3277 12983.6697 0.0000
0.0000 -2525607.1884 832652.3203 0.0000
0.0000 0.0000 -1536507.8707 0.0000 -1536507.8707
-1536507.8707 0.0000 9770920.1156 9774414.2593
1208309.6819 9770920.1156 9774414.2593

     However, it reports "bad global exclusion" when I run the following
simulation of raising temperature on the workstation.

     Can anyone give some explanations?

     Thanks and Best wishes!

Yuhui

-- 
Ph. D Yuhui He (ع)
Institute of Scientific and Industrial Research, Osaka University;
Mihogaoka 8-1, Ibaraki, Osaka 567-0047. JAPAN

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