[gmx-users] protein wandering away

[David]

On Wed, 2005-03-23 at 10:37 -0800, Nancy Deng wrote:
> Dear All,
> 
> I just simulated a 5ns MD by GROMACS FF for a small system containing 160
> amino acid residues in a water box. The thing confused me was that the
> protein started to close one edge of the water box around 2ns and part of it
> movedout of the box later. At the end of the 5ns calculation, most of
> protein was out of the box, while water molecules were still in the box.
> 
> I use "pbc =xyz", and also other parameters as pasted below for your
> opinion. I am just wandering whether I need to re-assign velocity. If so, by
> how???  Highly appreciate any of your suggestions.
> 
this is correct behviour. the protein is still in the box.

don't change velocitoes.
> Nancy
> 
> ************  the "5ns.mdp" file pasted below************
> title               =  5ns
> cpp                 =  /usr/bin/cpp
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  2500000; 5ns
> constraint-algorithm = shake
> nstcomm             =  1
> nstxout             =  500
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  500
> nstenergy           =  500
> nstlist             =  10
> ns_type             =  grid
> coulombtype         =  PME
> rlist               =  0.9
> rcoulomb            =  0.9
> rvdw                =  0.9
> fourierspacing      =  0.12
> pme_order           =  4
> optimize_fft        =  yes
> pbc                 = xyz
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc-grps             =   Protein  SOL  CL
> tau_t               =   0.1      0.1   0.1
> ref_t               =   300      300   300
> ; Energy monitoring
> energygrps          =  Protein SOL  CL
> ; Pressure coupling is not on
> Pcoupl              =  berendsen
> pcoupltype          =  isotropic
> tau_p               =  1
> compressibility     =  4.5e-5
> ref_p               =  1
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
> 
> ******end of attachment*********
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++