[gmx-users] Problem regarding Complex ion addition by genbox
kinshuk at chem.iitb.ac.in
kinshuk at chem.iitb.ac.in
Mon Jan 28 11:00:21 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.?
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
>> atom
>> 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
>> all
>> 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
> (protein.gro).
>
> 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
> protein_guanidinium_tip3p.gro
>
> 5. EM
>
> 6. Posre ME
>
> 7. MD
>
> Hope it helps,
> Chris.
>
>>> I tried with genbox option with perticular concentration i.e.
>>> perticular
>>> 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
>>> contacts
>>> 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
>> happens?
>>
>> Chris.
>>
>>> i reduced the time steps in pr.mdp from .002 to .001 ps file but again
>>> it
>>> shows the same problem. i have seen the pdb files after genbox really
>>> some
>>> close contacts between was there it means insertion of extra molecule
>>> by
>>> 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
>>> added
>>> in genion steps. Only change in new system (guanidium ion, SCN- ,
>>> water,
>>> peptide) is of SCN-. Addition of SCN- in genbox step is creating
>>> problem.
>>> 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
>>> (yes,no)
>>> 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
>>>> ion
>>>> &
>>>> thiocynate ion(SCN-).I tried to add these ion by genion command line
>>>> by
>>>> 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
>>>> for
>>>> monoatomic ion.
>>>> If i have to do simulation with these polyatomic ions with
>>>> perticular
>>>> salt concentration how do i will perform it.
>>>>
>>> with genbox. compute number yourself.
>>>>
>>>> Kinshuk
>>>> IIT-Bombay
>>>> India
>
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