[gmx-users] seperating bilayers (again)

[Eric Jakobsson]

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