[gmx-users] polyatomic ion additon by genion & genbox

[kinshuk at chem.iitb.ac.in]

---------------------------- Original Message ----------------------------
Subject: Re: [gmx-users] polyatomic ion additon by genion
From:    kinshuk at chem.iitb.ac.in
Date:    Thu, January 24, 2008 10:34 am
To:      "Discussion list for GROMACS users" <gmx-users at gromacs.org>
--------------------------------------------------------------------------

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.

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
>
>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> _______________________________________________
> 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
>