[gmx-users] Problems in gromacs
karamyog singh
karamyog.singh at gmail.com
Wed May 10 12:20:51 CEST 2006
Thanks a lot! :)
On 5/10/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> karamyog singh wrote:
> > Greeting gromacs users. I am trying to use gromacs to simulate metals. I
> > am trying to simulate BCC Iron. But I get the following error message.
> >
> > Fatal error: Invalid order for directive moleculetype, file
> > ""topol.top"", line 5
>
> read chapter 5 in the manual about topology files.
>
> >
> > I am sending you my input files. Please help me and tell me what is
> > wrong with my files. Also can you tell me if it is possible to simulate
> > metallic crystals using gromacs. Mostly people have worked on Bio
> > Molecules. However I believe that I should be able to simulate Metallic
> > structures if I modify the source codes a bit. Also, Can you please tell
> > me if I can use my own potential functions?
> Depends on what you want. CHeck manual on tabulated functions.
>
>
> >
> > I downloaded force fields made by other people, I have modified them
> > too to include xb_1 bond type and FE FE interaction. These modifications
> > have been done in ffG53a6.rtp and ffG53a6bon.itp. These files are in
> > 53a6.tar.gz on the force field download section of the website
> > www.gromacs.org <http://www.gromacs.org>.
> >
> > I request you to please help me out as soon as you can. :)
> >
> >
> > ------------------------------------------
> > grompp.mdp
> >
> > NES STARTING WITH ';' ARE COMMENTS
> > title = Minimization of Hen Egg White Lysozyme (1AKI.pdb)
> > ; Title of run
> >
> > ; The following lines tell the program the standard locations where to
> > find certain files
> > cpp = /lib/cpp ; Preprocessor
> > include = -I../top ; Directories to include in the topology
> > format
> >
> > ; Parameters describing what to do, when to stop and what to save
> > integrator = steep ; Algorithm (steep = steepest descent
> > minimization)
> > emtol = 1.0 ; Stop minimization when the maximum
> > force < 1.0 kJ/mol
> > nsteps = 200 ; Maximum number of (minimization) steps
> > to perform
> > nstenergy = 10 ; Write energies to disk every nstenergy
> > steps
> > nstxtcout = 10 ; Write coordinates to disk every
> > nstxtcout steps
> > xtc_grps = Protein ; Which coordinate group(s) to write to
> disk
> > energygrps = Protein ; Which energy group(s) to write to disk
> >
> > ; Parameters describing how to find the neighbors of each atom and how
> > to calculate the interactions
> > nstlist = 5 ; Frequency to update the neighbor list
> > and long range forces
> > ns_type = simple ; Method to determine neighbor list
> > (simple, grid)
> > rlist = 1.0 ; Cut-off for making neighbor list
> > (short range forces)
> > coulombtype = cut-off ; Treatment of long range electrostatic
> > interactions
> > rcoulomb = 1.0 ; long range electrostatic cut-off
> > rvdw = 1.0 ; long range Van der Waals cut-off
> > constraints = none ; Bond types to replace by constraints
> > pbc = yes ; Periodic Boundary Conditions (yes/no)
> > ----------------------------------------------
> > topol.top
> > #include "ffG53a6.itp"
> > ;#include "ffgmx.rtp"
> > ;#include "ffgmx.atp"
> >
> > [ moleculetype ]
> > Ions 3
> >
> > [ atoms ]
> > 1 Fe 1 HEME FE 1 0 55.870
> > 2 Fe 2 HEME FE 1 0 55.870
> > 3 Fe 3 HEME FE 1 0 55.870
> > 4 Fe 4 HEME FE 2 0 55.870
> > 5 Fe 5 HEME FE 2 0 55.870
> > 6 Fe 6 HEME FE 2 0 55.870
> > 7 Fe 7 HEME FE 2 0 55.870
> > 8 Fe 8 HEME FE 3 0 55.870
> > 9 Fe 9 HEME FE 3 0 55.870
> >
> > [ bonds ]
> >
> > 1 2 1 0.1000 1.7800e+7
> > --------------------------------------------------
> > Pure Fe
> > 9
> > 1Fe FE 1 0.00 0.00 0.00 0.000 0.000 0.000
> > 2Fe FE 2 2.70 0.00 0.00 0.000 0.000 0.000
> > 3Fe FE 3 0.00 2.70 0.00 0.000 0.000 0.000
> > 4Fe FE 4 0.00 0.00 2.70 0.000 0.000 0.000
> > 5Fe FE 5 0.00 2.70 2.70 0.000 0.000 0.000
> > 6Fe FE 6 2.70 0.00 2.70 0.000 0.000 0.000
> > 7Fe FE 7 2.70 2.70 0.00 0.000 0.000 0.000
> > 8Fe FE 8 2.70 2.70 2.70 0.000 0.000 0.000
> > 9Fe FE 9 1.35 1.35 1.35 0.000 0.000 0.000
> >
> >
> > conf.gro
> >
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
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>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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