[gmx-users] parameters problem

[Justin Lemkul]

On 2/17/14, 4:16 AM, Nidhi Katyal 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.
>

The more relevant information is which force field you are using.  It is also 
possible that the introduction of pressure coupling without restraints can cause 
screwy behavior, so a restrained NPT equilibration is probably worthwhile, as well.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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