[gmx-users] Problem regarding Complex ion addition by genbox
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Mon Jan 28 17:00:42 CET 2008
> Thanks a lotfor responding me.Sorry for complexity.
> As you have suggest that in step 2.
> (2. Use editconf to put your guanidinium ion in a box of such a size so)>
> In input X.gro file in editconf there will be one guanidium ion or total
> number of guanidium ion that is required for desired concentration.
> How many guanidinium ion we will put in box & How to generate input .gro
> file in editconf in step 2 of your's siggested step.?
That is up to you. Read about genbox and you will see that you could
go either route if you wanted. The method that I suggested was for a
single ion in a box. Try that. Go ahead and use genconf if you want,
but that would be outside of what I have suggested. If you have
difficulty then make a test system with no protein, just an empty box
of desired size to start, and go through the procedure that I outlined
to see how it works.
> I have used genconf in that i used to give X.gro file contaning
> information of one molecule.It multiplies a given coordinates file.Will
> this help or which is most appropriate way to generate input .gro file
> in editconf in step 2?
> In step 4 it will add water molecule according to box size.How we will
> control it for desired concentration.
>> that it is at the desired concentration (guanidinium.gro).
>> Thanks for giving me insight. But i have a query.
>> I tried to add complex ion by genion but while adding, it replaces the
>> water molecule according to my choice but it shows information of one
>> only not of all atom of that complex molecule in structure file (.gro).i
>> then tried to use by genbox.How should it will display information of
>> atom of complex molecule ?
> I'll do my best to answer, but if you want some better help then I am
> afraid that you need to find somebody on your end that can assist you
> in getting the question across in english that is more easily
> understood. Unfortunately I do not understand your particular question
> on this post, I only assume that you still don't have the answer.
> Here is what I would first think of doing (but I have never tried it).
> 1. Use editconf to put your protein in the box of desired size
> 2. Use editconf to put your guanidinium ion in a box of such a size so
> that it is at the desired concentration (guanidinium.gro).
> 3. genbox -cp protein.gro -cs guanidinium.gro -o protein_guanidinium.gro
> 4. grnbox -cp protein_guanidinium.gro -cs tip3p.gro -o
> 5. EM
> 6. Posre ME
> 7. MD
> Hope it helps,
>>> I tried with genbox option with perticular concentration i.e.
>>> number of each component like guanidium ion thiocynate ion & water
>>> molecule.But while doing PR(position restrain MD) it showing errors :
>>> constraints errors in algorithm shake at step 0. t=o.oo ps : water
>>> molecule starting at atom 3010 can not be settled. check for bad
>>> and/or reduce the time steps.
>> Quote from 'genion -h',
>> "For larger ions, e.g. sulfate we recommended to use genbox."
>> If you must use genion for some reason then the only question I see is:
>> Did you do EM? If not then try that first. Also, for genion or genbox,
>> you might try simplifying your system. Take a box of water and use
>> genion to add a single guanidium. Then EM, then MD (dt=0.002). What
>>> i reduced the time steps in pr.mdp from .002 to .001 ps file but again
>>> shows the same problem. i have seen the pdb files after genbox really
>>> close contacts between was there it means insertion of extra molecule
>>> gen box is not proper it leads to some bad contacts.
>>> The real problem is that when performing simulation of peptide with
>>> guanidium ion , CL- , water it is showing no problem because CL- is
>>> in genion steps. Only change in new system (guanidium ion, SCN- ,
>>> peptide) is of SCN-. Addition of SCN- in genbox step is creating
>>> Is any other method to perform simulation of peptide in solvent systrm
>>> (guanidium ion, SCN-, water).
>>> Please give me some insight to resolve this issue.
>>> This is pr.mdp file
>>> title = Nanomer ; a string
>>> cpp = /lib/cpp ; c-preprocessor
>>> define = -DPOSRES
>>> dt = 0.001 ; time step
>>> integrator = md
>>> tinit = 0.0
>>> nsteps = 100000 ; number of steps
>>> nstcomm = 1 ; reset c.o.m. motion
>>> nstxout = 500 ; write coords
>>> nstvout = 500 ; write velocities
>>> nstfout = 0
>>> nstlog = 500 ; print to logfile
>>> nstenergy = 500 ; print energies
>>> nstlist = 10 ; update pairlist
>>> ; Neighbour Searching
>>> ns_type = grid ; pairlist method
>>> ; Electrostatics and VdW
>>> coulombtype = PME
>>> vdwtype = shift
>>> rlist = 1.5 ; cut-off for ns
>>> rvdw_switch = 0.8
>>> rvdw = 1.4 ; cut-off for vdw
>>> rcoulomb_switch = 0.8
>>> rcoulomb = 1.5 ; cut-off for coulomb
>>> ;Temperature coupling
>>> Tcoupl = berendsen ; temperature bath
>>> ref_t = 298 298
>>> tc-grps = Protein Non-Protein
>>> tau_t = 0.1 0.1
>>> ; Pressure coupling
>>> Pcoupl = no ; pressure bath
>>> tau_p = 0.5
>>> compressibility = 4.5e-5
>>> ref_p = 1.0
>>> ; Velocity generation
>>> gen_vel = yes ; generate initial
>>> gen_temp = 298.0 ; initial temperature
>>> gen_seed = 173529 ; random seed
>>> constraints = all-bonds
>>> constraint_algorithm = shake
>>> shake_tol = 0.0001
>>> kinshuk at chem.iitb.ac.in wrote:
>>>> Hi all,
>>>> I have been trying to simulate peptide in water box with guanidium
>>>> thiocynate ion(SCN-).I tried to add these ion by genion command line
>>>> simply adding topology information of these ion in ions.itp of gromacs
>>>> library directory but it is not working properly it only adds one atom
>>>> by replacing water molecule it seems that genion is applicable only
>>>> monoatomic ion.
>>>> If i have to do simulation with these polyatomic ions with
>>>> salt concentration how do i will perform it.
>>> with genbox. compute number yourself.
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