[gmx-users] seperating bilayers (again)

[Alan Dodd]

15, 20, even 30 nm all result in the same effect, just
at different rates.  I didn't try anything larger than
that - several of my systems would be dangerously
close to being under 2x the cutoff radius across if I
went even slightly higher.

--- Eric Jakobsson <jake at ncsa.uiuc.edu> wrote:

> What is your van der Waals cut-off distance? From
> our experience 
> years ago, we sometimes saw this if our van der
> Waals cut-off was too 
> short; i.e., less than 15 angstroms.  That seems
> long, since it falls 
> off as sixth power, but because the long-range van
> der Waals is all 
> attractive, there is no shielding (unlike the
> electrostatic force).
> 
> At 11:03 AM 4/6/2006, you wrote:
> >Hello all,
> >I've been having some trouble recently with the
> >leaflets in my bilayer gently drifting apart over a
> >period of a few hundred picoseconds.  Increasing
> the
> >vdW radius hasn't helped (up to 2nm), although it
> did
> >delay the seperation.  Likewise, increasing tau_p
> from
> >5 up to 10.  The really bizarre thing is that I've
> >been simulating peptides in bilayers using 3.2.1 on
> >our cluster for about 18 months now, using the
> >lipid-modified version of ffgmx and the parameters
> >listed below, and it's only since I've started
> using
> >3.3 on a new machine that I've had any trouble. 
> Any
> >suggestions on what might be going wrong?
> >
> >title               =  Yo
> >cpp                 =  /lib/cpp
> >constraints         =  all-bonds
> >integrator          =  md
> >dt                  =  0.0015   ; ps !
> >nsteps              =  5000000  ; total 7500 ps.
> >nstcomm             =  1
> >nstxout             =  1000
> >nstvout             =  1000
> >nstfout             =  0
> >nstlog              =  1000
> >nstenergy           =  1000
> >nstlist             =  10
> >ns_type             =  grid
> >coulombtype         =  PME
> >rlist               =  1.5
> >rcoulomb            =  1.5
> >rvdw                =  1.5
> >pme_order           =  8
> >fourierspacing      =  0.2
> >optimize_fft        =  yes
> >; Berendsen temperature coupling is on in two
> groups
> >Tcoupl              =  berendsen
> >tc-grps             =  DOPC     SOL  Protein     
> Cl
> >tau_t               =  0.1      0.1      0.1    
> 0.1
> >ref_t               =  300      300      300    
> 300
> >; Energy monitoring
> >energygrps          =  DOPC     SOL  Protein
> >; Isotropic pressure coupling is now on
> >Pcoupl              = berendsen
> >Pcoupltype          = surface-tension
> >tau_p               =  5
> >compressibility     =  4.5e-5 4.5e-5
> >ref_p               =  410 1.0
> >; Generate velocites is off at 300 K.
> >gen_vel             =  no
> >gen_temp            =  300.0
> >gen_seed            =  173529
> >
> >
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> ---------------------------------
> Eric Jakobsson, Ph.D.
> Professor, Department of Molecular and Integrative
> Physiology, and of 
> Biochemistry, and of the Center for Biophysics and
> Computational Biology
> Senior Research Scientist, National Center for
> Supercomputing Applications
> Professor, Beckman Institute for Advanced Science
> and Technology
> 3261 Beckman Institute, mc251
> University of Illinois, Urbana, IL 61801
> ph. 217-244-2896       fax 217-244-2909
> 
> 
> 
> 
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