Chih-Ying Lin wrote:
HI
When I run MD, my system is exploding.
And, I found after minimisation, the atoms of my molecule are seperated apart.
That probably suggests that whatever parameters you've applied are not correct.
The overall charge of my system is +1, and I put one molecule in the
gas phase to do the structure test. But, it was already exploding.
What is a "structure test"? What are you trying to determine?
Is it hard for a +1 charge molecule to maintain a good shape under MD
simulation?
Gas-phase charges involve high-energy species (ionized mass spec samples,
plasma, etc.), so the answer is probably yes.
What is your molecule? Is it a protein? If you're using a charged protein in a
vacuum, the force field you're using may not be valid.
-Justin
What are the procedures to test and determine the mistakes I made?
Thank you
Lin
Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file fullmd.tpr, VERSION 3.3.3 (single precision)
Loaded with Money
starting mdrun 'azoct'
100000 steps, 100.0 ps.
Warning: 1-4 interaction between 11 and 18 at distance 1.301 which is
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
step 10, will finish at Sun Oct 5 06:17:20 2008
-------------------------------------------------------
Program mdrun, VERSION 3.3.3
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 5832 ]
-------------------------------------------------------
"She's Not Bad, She's Just Genetically Mean" (Captain Beefheart)
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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