namd hangs

From: Uma Mahankali (umamahankali_at_gmail.com)
Date: Mon Aug 08 2005 - 23:10:13 CDT

• Next message: Edelmiro Moman: "How to "extract" coordinates from a DCD trajectory file?"
• Previous message: Jason Lee: "Charmm++5.9 build on Mac OS X by IB xlc compiler"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello,

I have been trying to run an MD simulation with constraints.
Every time namd hangs at the point
-----------------------------------------------------------------------------
Info: NONZERO IMPRECISION IN COULOMB TABLE: 1.11022e-16 3.55271e-15
Info: Entering startup phase 8 with 38812 kB of memory in use.
Info: Finished startup with 40940 kB of memory in use.
TCL: Running for 100000 steps
ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC KINETIC TOTAL
TEMP PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 100000 131.0724 3462.7498 460.5130 0.4957
-240840.0461 22585.0386 41282.6718 0.0000 28703.5211
-144213.9836 287.3309 12049.4203 -312.7764 864000.0000
12049.4203 -312.7764
OPENING EXTENDED SYSTEM TRAJECTORY FILE
----------------------------------------------

I have some atoms fixed and some atoms constrained... I am not sure if
there are specific rules to follow when using both options.My
simulation runs fine when I use just the fixed atoms option.

When I tried to change some of the constraints, the simulation crashed
reporting a rattle algorithm error.
 
Can someone please suggest how to figure what's going wrong?

Thanks,
Uma Mahankali
Cincinnati,
Ohio

• Next message: Edelmiro Moman: "How to "extract" coordinates from a DCD trajectory file?"
• Previous message: Jason Lee: "Charmm++5.9 build on Mac OS X by IB xlc compiler"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:49 CST