Unstable atoms

From: Ale Gomez (agomez_at_physics.org)
Date: Sat Mar 06 2010 - 23:00:30 CST

Hi everybody.
I am studying a system between bacteriorhodopsin and a lipid membrane. First
I minimize my system at 10000 steps. Then I wanted to warm it up with this
config file

*structure ../Minimizacion/bRET_final.psf*
*coordinates ../Minimizacion/bRET_final.pdb*
*bincoordinates ../Minimizacion/bRETmin.coor*
*extendedSystem ../Minimizacion/bRETmin.xsc*
*outputName bRETcal*
*
*
*firsttimestep 0*
*
*
*#############################################################^M*
*## SIMULATION PARAMETERS ##^M*
*#############################################################^M*
*
*
*# Input*
*paraTypeCharmm on*
*parameters ../par_all27_prot_lipid_ret.prm*
*
*
*# Force-Field Parameters*
*exclude scaled1-4*
*1-4scaling 1.0*
*cutoff 14.*
*switchdist 10.*
*pairlistdist 15*
*margin 0*
*
*
*# Integrator Parameters*
*timestep 1.0 ;# 1fs/step*
*rigidBonds all ;# needed for 1fs steps*
*fullElectFrequency 4*
*stepspercycle 20*
*
*
*# Output*
*dcdfreq 500*
*outputEnergies 100*
*
*
*# Protocolo (calentamiento)*
*temperature 0*
*reassignFreq 25*
*reassignIncr 0.375*
*reassignHold 300*
*
*
*#############################################################^M*
*## EXTRA PARAMETERS ##^M*
*#############################################################^M*
*
*
*wrapAll on*
*
*
*#PME (for full-system periodic electrostatics)*
*PME yes*
*PMEGridSizeX 64*
*PMEGridSizeY 128*
*PMEGridSizeZ 128*
*
*
*#############################################################^M*
*## EXECUTION SCRIPT ##^M*
*#############################################################^M*
*run 20000*

But it didn't work because in my log file I always have this message:
*ERROR: Constraint failure in RATTLE algorithm for atom 18237!*
*ERROR: Constraint failure; simulation has become unstable.*
*ERROR: Exiting prematurely.*

When I tried to fix this atom and run it again, I got another error message
with different atom. After some changes in my configuration, I figured it
out that this message disappears when I fix the entire protein, but as you
can imagine, this assumption is wrong. Someone have any idea about it???.

Thanks in advance for your help.
Kind Regards

-------------------------------------------------------------------
Ale Gomez
Biophysics and Molecular Modeling Group
Physics Department
Escuela Politecnica Nacional, Quito-Ecuador
Ladron de Guevara E11-253.
Phone: 593-95292408
http://www.ciencias.epn.edu.ec/~biomod/

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:47 CST