[gmx-users] Problem regarding Complex ion addition by genbox

[kinshuk at chem.iitb.ac.in]

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 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
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>