Re: NVT system implosion!!!

From: Marco Preto <>
Date: Wed, 30 Oct 2002 18:46:07 +0000

Dear Amber users:

Well, after banging my head to a wall several times :-), and following a
clue from a more experienced colegue, I went to check the parameters
used for Cl- (atom type IM in the parm96.dat). We've noticed that in
this version of the force feild, the VDW parameters for this ions are
both 0 (zero). I've hedded the parameters from parm94 to my frcmod file
and now the NVTsimulation is running OK!
But one thing still intriges me! Cl- would be a pure atractor for all
positive charged atoms, and they would be atracted to Cl-, but wouldn't
we expect repulsions from all the other atoms (because this had VDW
parameters diferent from zero)?

Thank you for all your attention


Marco Preto

Marco Preto wrote:

> Dear amber users:
> I presently doing some simulations of small peptides (8 aa) in a water
> box (around 3850 water molecules, PME implementation for long range NB
> interactions), using sander (from AMBER 6).
> Firtly I performed a minimization of the solvent (fixing the positions
> of the the solute and Cl- counter ion). The geometry output from the
> minimization is OK.
> Secondly, I was planning to perform a NVT equilibration on the same
> system (temp gradient from 0 to 300K and aplying harmonic constrains
> to the solute ( peptide and counter ion). The molecular dynamic run to
> the end without any error message, but when I checked the last
> geometry, EVERY atom was possitioned in the Origin (0,0,0
> coordinates)!!!???!!! I tryed the same simulation without the
> constrains (I could have donne some mistake in the group definition!)
> but got the same result! This implosion ocours very quickly in the
> first 100 some fs! Have anyone encoutered any problem like this?
> Here are the inputfile for the minimization and the NVT dynamic run:
> Min:
> &cntrl
> imin=1, maxcyc=2000, cut=12, igb=0,
> ntb=1, ntpr=500, ncyc=200,
> ibelly=1, ntc=2, ntf=2,
> &end
> Group input for moving atoms
> RES 10 3846
> NVT Dyn:
> &cntrl
> imin=0, irest=0, ntx=1, tempi=0,
> nstlim=50000, dt=0.001,
> cut=12.0,
> ntt=1, temp0=300.0, tautp=1,
> ntp=0,
> ntpr=200, ntwe=200, ntwx=200,
> ntb=1, ntc=2, ntf=2, ntr=1,
> ioutfm=0
> &end
> Group input for restrained atoms
> 1.0
> RES 1 9
> Thanks for all the help
> Sincerely

 Marco A. C. Preto               |"Quantum temporis lucratur qui non
 PH.D. student                   |aspicit quod vicinus dicit, agit
 Theoretical Chemistry group     |vel cogitat, sed tantum quod ipse
 Chemistry Deparmant - FCUP      |agit ad id iustum et sanctum 
 Porto, Portugal                 |reddendum"
                                 |   from my homonimous
email:          |  
                                 |                 Marcus Aurelius
Received on Thu May 29 2003 - 09:53:00 PDT
Custom Search