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 > [EMAIL PROTECTED] 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@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 [EMAIL PROTECTED] >> 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. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
