[gmx-users] parameters problem

[Mark Abraham]

Seems like you're using cut-off electrostatics, which would be a good way
of picking lottery numbers, and that's about all.

Mark


On Mon, Feb 17, 2014 at 10:16 AM, Nidhi Katyal <nidhikatyal1989 at gmail.com>wrote:

> Dear all
>
> I am trying to simulate a protein in 3 steps: energy minimization (using
> em.mdp), position restraints (using pr.mdp) and final production run by NPT
> ensemble (using full.mdp) at 300K
>
> At this temperature, it is known by previous literature survey that protein
> keeps its secondary structure almost intact. But according to my
> simulations (done thrice), protein starts loosing its secondary structure
> around 6-8ns only. I have used the following parameters:
>
> *em.mdp*
>
> ;
> ;     User spoel (236)
> ;     Wed Nov  3 17:12:44 1993
> ;     Input file
> ;
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> nsteps              =  250000
> ;
> ;     Energy minimizing stuff
> ;
> emtol               =  2000
> emstep              =  0.001
>
> nstcomm             =  1
> ns_type             =  grid
> rlist               =  1
> rcoulomb            =  1.0
> rvdw                =  1.0
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
>
>
> *pr.mdp*
>
> ;
> ;     User spoel (236)
> ;     Wed Nov  3 17:12:44 1993
> ;     Input file
> ;
> title               =  Yo
> cpp                 =  /usr/bin/cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002  ; ps !
> nsteps              =  50000  ; total 100 ps.
> nstcomm             =  1
> nstxout             =  5000
> nstvout             =  5000
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc-grps               =  Protein    Non-protein
> tau_t               =  0.1    0.1
> ref_t               =  300    300
> ; Energy monitoring
> energygrps      =  Protein    Non-protein
> ; Pressure coupling is not on
> Pcoupl              =  no
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
>
>
> *full.mdp*
>
> ;
> ;     User spoel (236)
> ;     Wed Nov  3 17:12:44 1993
> ;     Input file
> ;
> title               =  Yo
> cpp                 =  /usr/bin/cpp
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002  ; ps !
> nsteps              = 25000000      ; total 50000 ps.
> nstcomm             =  1
> nstxout             =  5000
> nstvout             =  5000
> nstfout             =  0
> nstlog              =  5000
> nstenergy           =  5000
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc-grps               =  Protein Non-protein
> tau_t               =  0.1    0.1
> ref_t               =  300      300
> ; Energy monitoring
> energygrps          =  Protein  Non-protein
> ; 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
>
>  I don't think it is the problem of thermostat because even after using
> V-rescale for temperature coupling and Parinello Rahman for pressure
> coupling, my protein loses its secondary structure in the initial time of
> simulation.
>
> Also, I have carried out various checks (like potential energy convergence
> after em, temperature check after pr, and pressure and density check after
> full), all of which seems to converge well.
>
> Please help me figure out the problem.
> --
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