[gmx-users] IONs + PME run problem!!

[Mungikar, Amol Arvind (UMR-Student)]

Dr.Spoel,

No the runs are not made on ATHLON, they are on P-4 ....

I thought I should show you the energies at 382 ps (the blowing of energy occurs at 383 ps), they look correct to me, and suddenly the energies are going way high. Clearly there is a overlap or bad contact, this is precisely what I wanted to ask. How can i avoid this? 

Step Time Lambda Annealing

191000 382.00003 0.00000 1.00000

Rel. Constraint Deviation: Max between atoms RMS

Before LINCS 0.021390 1 2 0.003328

After LINCS 0.000046 37 39 0.000024

Energies (kJ/mol)

Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14

1.36838e+02 5.20855e+01 4.21964e+01 2.31527e+01 1.18576e+03

LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En.

4.37105e+03 -3.23185e+04 -5.72217e+03 -3.22296e+04 5.10971e+03

Total Energy Temperature Pressure (bar)

-2.71199e+04 2.93203e+02 -1.39508e+03

	> 
	> MD run output:
	> t = 383.000 ps: Water molecule starting at atom 1300 can not be settled.
	>
	> Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
	>
	> Energies (kJ/mol)
	>
	> Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
	>
	> 1.10620e+02 5.17073e+01 5.82271e+01 3.68468e+01 1.18949e+03
	>
	> LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic En.
	>
	> 2.35068e+06 -3.19766e+04 -5.70743e+03 2.31444e+06 nan
	
	energy is way off. is this running on an athlon?
	
	>
	> Total Energy Temperature Pressure (bar)
	>
	> nan nan nan
	>
	> Fatal error: ci = -2147483648 should be in 0 .. 124 [FILE nsgrid.c, LINE 210]
	>
	> It says me to reduce the timestep, I didnt understand this, why?
	>
	> Am I doing anything wrong with "md.mdp" file!! or the energy minimization is creating a problem.
	>
	> Thank you very much for your help!
	>
	> Amol A Mungikar
	>
	> 
	>
	> 왨x%`
	> 虧,iஉrj)fjb?lǫ^jǝ?-rz--bԱa{ 0{^zzwb -
	> 虧,
	--
	David.
	________________________________________________________________________
	David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
	Dept. of Cell and Molecular Biology, Uppsala University.
	Husargatan 3, Box 596,          75124 Uppsala, Sweden
	phone:  46 18 471 4205          fax: 46 18 511 755
	spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
	
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