[gmx-users] Is something wrong wih my mdp?

[Mark Abraham]

Don't use position restraints or generate velocities after equilibration!
Nor should you couple ions to their own
http://www.gromacs.org/Documentation/Terminology/Thermostats

Mark
On Apr 8, 2014 6:21 AM, "chenxianli" <1471769256 at qq.com> wrote:

> Hi all!
>   Recently I have been doing the MD simulation about the ratio of opening
> and closing of RNA base pais in different Na ion concentrations. Runing 20
> ns simulation using  Gromacs.
>
> As far as I know,in most articles on this problem saying: the higher Na ion
> concentration ,the more stable of RNA structure,so the probility of base
> pair opening will decrease .But I can't get the same results...  Does
> anyone
> konw why ?
> After runing equilibrium, my mdp file is as follows:
>
>
>
> title                   = 1ZIH
> define                   = -DPOSRES
> cpp                     = /lib/cpp
> constraints             = all-bonds
> ;run parameters
> integrator          =  md
> dt                  =  0.002                       ; ps
> nsteps              =  1000000                 ; total 0.2ns
> nstcomm             =  100
> ;output control
> nstxout             =  1000                     ; collect data every 2 ps
> nstxtcout           =  1000
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  1000
> nstcalcenergy       =  100                     ;frequency fo calculating
> the
> energy
> nstenergy           =  1000                    ;frequency to write energies
> to energy file
> ;Bond parameter
> continuation           = no                     ;no constant restarting
> constraint-algorithm   = lincs
> lincs_iter             = 1
> lincs_order            = 4
> ;Neighborsearching
> ns_type                =  grid
> nstlist                =  5
> rlist                  =  1.0
> rcoulomb               =  1.0
> vdwtype                =  cut-off
> rvdw                   =  1.0
> ;Electrostatics
> coulombtype          =  PME
> pme_order             =  4
> fourierspacing        =  0.12
>
> ;Temperature coupling is on
> Tcoupl              = V-rescale                     ;berendsen
> tc-grps             = RNA      SOL    NA   CL
> Tau_t               = 0.1      0.1   0.1   0.1
> ref_t               = 350      350   350   350
>
> ; Berendsen  Pressure coupling is on
> Pcoupl                  = Parrinello-Rahman
> refcoord-scaling        = all
> Pcoupltype              = isotropic
> tau_p                   = 0.5
> compressibility         = 4.5e-05
> ref_p                   = 1.0
>
> ;Periodic boundary conditions
> pbc                     = xyz
>
> ;Dispersion correction
> DispCorr                = EnerPres
>
> ; Generate velocites is on at 300 450 500 550 K.
> gen_vel                 = yes
> gen_temp                = 350
> gen_seed                = 173529
>
>
> Is something wrong with my mdp file?
> Thanks ！
>
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