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

[Mark Abraham]

Also, why do you consider 20ns a significant time over which to observe
multiple open and closed states from which to gather statistics?

Mark


On Tue, Apr 8, 2014 at 9:47 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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 ！
>>
>> --
>> View this message in context:
>> http://gromacs.5086.x6.nabble.com/Is-something-wrong-wih-my-mdp-tp5015715.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>> --
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>