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

[chris.neale at utoronto.ca]

> 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