[gmx-users] (no subject)

[Bert de Groot]

Nguyen Hoang Phuong wrote:


> first, you have to use double precision.
> Here is an example of mdp file.
> title                    = protein in water
> cpp                      = /lib/cpp
> include                  = -I../top
> define                   = -DFLEX_SPC
> integrator               = cg
> emtol                    = 0.000001
> emstep                   = 0.000001
> nstcgsteep               = 100
> nsteps                   = 500000
> nstxout                  = 50
> xtc_grps                 = Protein
> energygrps               = Protein
> nstlist                  = 10
> ns_type                  = grid
> rlist                    = 1.4
> vdwtype                  = Shift
> coulombtype              = PME
> rcoulomb                 = 1.4
> rvdw                     = 1.4


hmm, I don't think PME should be used in NM, either in vacuum or a water shell.
The interactions with the (infinite number of) periodic images would
be artificial (and more harmful than in a solvent MD simulation, with the
screening effect of the water instead of the vacuum here). Moreover, the
interactions with the periodic images might make the minimization less stable.

Better use a large enough cutoff, to include the whole system 
(AND a large enough box to prevent interactions with periodic images, or
switch off PBC alltogether).


> 
> in vacuum, you can easily get the mimimum energy structure but in
> water it will take a lot of time. You can look at the value of Fmax which
> is printed out for every step. If Fmax<10^5 then you may have the optimal
> structure. 

that should be a 10^-5 I guess?


-- 

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________