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

[Kalyan Reddy]

You have mentioned that you are doing the MD simulation about the ratio of
opening and closing of RNA base pais in different Na ion concentrations.
Then I don't think at the final MD run, position restraining of RNA is a
good idea here.

You didn't mentioned which force field you are using. It is known that for
DNA/RNA, most widely used forcefields are AMBER and CHARMM. If you use any
of them,  "*constraints= h-bonds*" is sufficient.

And this is not a 20ns simulation. nsteps seems to be a 2ns simulation.

Velocities are generated (follows Maxwell distribution) in the
equilibration step. Do not generate velocities after equilibration step.

Yes, it is true that number and type of ions is important in DNA/RNA
simulations, because they play a major role in maintaining stability RNA.
Understanding your aim of simulation and from my experience, I can say that
20ns simulation is very less time for your study. You can observe the role
of ions at a higher time scale.



On Tue, Apr 8, 2014 at 9:16 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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-- 

Kalyan Reddy