Re: error caused by atoms of lipid membrane

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Mon Mar 20 2006 - 10:35:14 CST

Hi Xiaojing,

I think the problem here is that you have fixedatoms turned on. (I've
noticed this problem too. For some reason, having fixed atoms on and
trying to apply constant pressure results in this hard error).

Instead of fixedatoms, you might want to try constraints. But even
then, you might get the rattle error; I've noticed that the more
stringent my constraints (i.e. 10 kcal force constant) the more likely
it is to crash. I'd set it to something like 2, or 5 at most.

Hope this helps,

Arneh

xiaojing gong wrote:

> *Dear all,*
> * Thank you for your suggestions that had given to me.*
> * I use the VMD 1.8.3 to produce membrane -x 100, -y 100, but
> there is still error warnings in VMD. First I ignore these errors, and
> do minimization.BUT when I do the equilibrium, there is fatal error*
> *stopping the simulation. could anyone give some suggestions. The
> atoms in the error messages is all the atoms of lipid. The attachment
> is my conf file. *
> TCL: Running for 300000 steps
> ETITLE: TS BOND ANGLE DIHED IMP
> ELECT VDW BOUNDARY MISC KINET
> TOTAL TEMP TOTAL2 TOTAL3 TEMPA
> PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSA
> ENERGY: 0 718.7559 5519.2091 6735.0556 133.34
> -163453.7739 12453.0185 0.0000 0.0000 99999999.99
> 99999999.9999 99999999.9999 99999999.9999 99999999.9999 99999999.99
> 99999999.9999 99999999.9999 1040600.0000 99999999.9999 99999999.99
> ERROR: Margin is too small for 12 atoms during timestep 1.
> ERROR: Incorrect nonbonded forces and energies may be calculated!
> ERROR: Constraint failure in RATTLE algorithm for atom 2277!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Atom 11674 velocity is 4121.86 -4942.28 -8445.38 (limit is 10000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Atom 14 velocity is -112846 69886.3 -79773.3 (limit is 10000)
> ERROR: Atoms moving too fast; simulation has become unstable.
>
> __________________________________________________
> ???????????????
> http://cn.mail.yahoo.com
>
>------------------------------------------------------------------------
>
>#forcefield
>paratypecharmm on
>parameters /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/min5000steps/par_all27_prot_lipid.inp
>#molecules
>structure /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/min5000steps/ions_added.psf
>coordinates /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/min5000steps/ions_added.pdb
>
>outputname /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/min5000steps/5000_min
>restartfreq 50
>DCDfile /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/min5000steps/5000_min.dcd
>DCDfreq 50
>binaryoutput yes
>binaryrestart yes
>outputEnergies 100
>wrapAll on
>wrapNearest on
>
>temperature 310
>
>#temp & pressure coupling
>langevin on
>langevinTemp 310
>langevinDamping 1
>
>
>#integrator
>timestep 1
>nonbondedFreq 2
>fullElectFrequency 4
>stepspercycle 20
>
>#approximations
>rigidBonds all
>rigidTolerance 0.00000001
>cutoff 12
>switching on
>switchdist 10
>pairlistdist 15
>margin 4.0
>exclude scaled1-4
>1-4scaling 1.0 # 1.0 for Charmm, 0.833333 for Amber
>
>cellBasisVector1 110 0. 0.
>cellBasisVector2 0. 110 0.
>cellBasisVector3 0. 0. 86
>cellOrigin 2.6 2.2 2.1
>
>PME on
>PMEProcessors 20
>PMEGridSizeX 110
>PMEGridSizeY 110
>PMEGridSizeZ 90
>
>fixedAtoms on
>fixedAtomsFile /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/min5000steps/fix_backbone.pdb
>fixedAtomsCol B
>
>#IMDon yes
>#IMDport 3000 ;# port number (enter it in VMD)
>#IMDfreq 1 ;# send every 1 frame
>#IMDwait on ;# wait for VMD to connect before running?
>
>#minimization on
>#minTinyStep 1.0e-6
>#minBabyStep 1.0e-2
>#minLineGoal 1.0e-4
>
>minimize 5000
>
>
>
>
>------------------------------------------------------------------------
>
>#forcefield
>paratypecharmm on
>parameters /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/par_all27_prot_lipid.inp
>
>#molecules
>structure /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/ions_added.psf
>coordinates /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/ions_added.pdb
>bincoordinates /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/5000_min.coor
>binvelocities /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/5000_min.vel
>#extendedSystem /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/5000_min.xsc
>
>cellBasisVector1 110 0. 0.
>cellBasisVector2 0. 110 0.
>cellBasisVector3 0. 0. 86
>cellOrigin 2.6 2.2 2.1
>
>#temperature 310
>#temp & pressure coupling
>langevin on
>langevinTemp 310
>langevinDamping 1
>
>useGroupPressure yes
>useFlexibleCell no
>LangevinPiston on
>LangevinPistonTarget 1.01325
>LangevinPistonPeriod 200
>LangevinPistonDecay 500
>LangevinPistonTemp 300
>
>#output
>outputname /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/300ps_sim
>outputEnergies 50
>restartfreq 100
>DCDfreq 100
>DCDfile /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/300ps_sim.dcd
>binaryoutput yes
>binaryrestart yes
>
>wrapAll on
>wrapNearest on
>
>#integrator
>timestep 1
>nonbondedFreq 2
>fullElectFrequency 4
>stepspercycle 20
>
>#approximations
>rigidBonds all
>rigidTolerance 0.00000001
>cutoff 12
>switching on
>switchdist 10
>pairlistdist 15
>margin 4.0
>exclude scaled1-4
>1-4scaling 1.0 # 1.0 for Charmm, 0.833333 for Amber
>
>
>PME on
>PMEProcessors 16
>PMEGridSizeX 110
>PMEGridSizeY 110
>PMEGridSizeZ 90
>
>fixedAtoms on
>fixedAtomsFile /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/300ps_fixrun/fix_backbone.pdb
>fixedAtomsCol B
>
>
>run 300000
>
>
>
>

-- 
----------------------------
Arneh Babakhani
University of California at San Diego
Physical Chemistry / Department of Chemistry & Biochemistry
Laboratory of Prof. J. A. McCammon
9500 Gilman Drive MC 0365
La Jolla, CA 92093-0365
(619)895-6540
(858)534-4974 (FAX)
http://mccammon.ucsd.edu/~ababakha/
ababakha_at_mccammon.ucsd.edu

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