[gmx-users] problem in pr.mdp file

[Justin A. Lemkul]

I think it might be more illustrative to understand why you think two different
systems will necessarily run at the same speed.  How large is the protein/water
system?  If it is a billion atoms and you expect it to run as fast as a system
containing only several thousand (running on the same number of processors),
then you would almost certainly be mistaken.

Also, note that in our temperature coupling section, you should not couple
solvent and ions separately.  See here:

http://wiki.gromacs.org/index.php/Thermostats

-Justin

Quoting sudheer <sudheer.pbm07 at gmail.com>:

>
> Thanks for response Mr.Alan Dodd
> 1) 1st run is simularion of position restrain of protein in water (25000
> steps)  - system running very very slow means for completion 10 steps it is
> taking more than 5 minutes or more
> 2) 2nd simulation is production step of popc in water (125000 steps ) - this
> is going normally means for completion 10 steps it is taking 3seconds or less
> than that.
> i will send you the both input files of pr.mdp and md.mdp files
>
> pr.mdp file ( This is already sent)
> title               =  Yo
> cpp                 =  /usr/bin/cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002
> nsteps              =  25000
> nstcomm             =  1
> nstxout             =  50
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
> pbc                 =  xyz
> ; Berendsen temperature coupling is on in two groups
> ; Pressure coupling is on
> Tcoupl              =  berendsen
> tc-grps             =  Protein   SOL    Na+
> tau_t               =  0.1       0.1    0.1
> ref_t               =  300       300    300
> Pcoupl              =  parrinello-rahman
> pcoupltype          =  isotropic
> ref_p               =  1
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ; Energy monitoring
> energygrps          =  Protein  SOL  Na+
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
>
>
> md.mdp file
> cpp = /lib/cpp
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 125000 ; total 250 ps.
> nstcomm = 1
> nstxout = 50
> nstvout = 10
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> rcoulomb = 1.0
> rvdw = 1.0
> pbc = xyz
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = berendsen
> tc-grps = POPC SOL
> tau_t = 0.1 0.1
> ref_t = 300 300
> ; Energy monitoring
> energygrps = POPC SOL
> ; Isotropic pressure coupling is now on
> Pcoupl = berendsen
> Pcoupltype = isotropic
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is off at 300 K.
> gen_vel = no
> gen_temp = 300.0
> gen_seed = 173529
>
>
>
> pls anyone help me
> thanks in advance.......



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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