[gmx-users] bond, angles and dihedrals in the topology file
faride badalkhani
farideh.khamseh at gmail.com
Sat Oct 3 20:29:33 CEST 2015
Thank you for your great help on specbond.dat file. I defined it and I
could go ahead until Energy minimization step. I have used this minim.mdp
file
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1000.0 ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to
perform
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and
long range forces
ns_type = grid ; Method to determine neighbor list
(simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list
(short range forces)
coulombtype = PME ; Treatment of long range electrostatic
interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
But when I run mdrun -v -deffnm em command, I get this error:
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 90 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -2.3956744e+05
Maximum force = 1.5824519e+05 on atom 380
Norm of force = 1.7695243e+03
gcq#187: "Been There, Done It" (Beavis and Butthead)
farideh at farideh-P61A-D3:~/FARIDEH$
I changed the emtol, emstep, and nsteps for a few times. However, I
couldn't resolve this problem. Could you tell me if there is something
wrong with the minim.mdp file?
You can see all the files via:
https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0
Truly yours,
Farideh
On Wed, Sep 30, 2015 at 9:13 PM, faride badalkhani <
farideh.khamseh at gmail.com> wrote:
> Dear Chandan,
> Thanks a lot for your answer.
> Truly yours,
> Farideh
>
>
> On Wednesday, September 30, 2015, Chandan Choudhury <iitdckc at gmail.com>
> wrote:
> > Dear Farideh,
> >
> > You may have a look at
> >
> https://code.google.com/p/molecular-simulation-of-soft-matter/issues/detail?id=1
> > for one such example.
> >
> > Chandan
> >
> > On Wed, Sep 30, 2015 at 8:29 PM, faride badalkhani <
> > farideh.khamseh at gmail.com> wrote:
> >
> >> Thank you for your time and answer. You are right, Dendrimers are
> composed
> >> of three main architectural components, a central core from which
> multiple
> >> arms emanate in an outward direction to form interior layers, and the
> >> reactive peripheral surface groups. Could you tell me if there is a
> sample
> >> specbond file for hyperbranched polymers?
> >>
> >> Regards,
> >> Farideh
> >>
> >> On Wed, Sep 30, 2015 at 6:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >> >
> >> >
> >> > On 9/30/15 8:24 AM, faride badalkhani wrote:
> >> >
> >> >> I want to simulate a dendrimer (a hyperbranched polymer) in water. I
> >> have
> >> >> used the GROMOS 53A6 force field parameters, and I have done the
> >> following
> >> >> steps:
> >> >> 1- Defining new atom types that were not exist in .atp file.
> >> >> 2- Adding appropriate bonds, angles, dihedrals, and impropers into
> the
> >> >> ffbonded.itp file.
> >> >> 3- Defining nonbonded parameters in ffnonbonded.itp file according to
> >> >> GROMOS FF parameters.
> >> >> 4- Introducing residue building blocks along with [bonds], [angles],
> >> >> [impropers], and [dihedrals] in .rtp file.
> >> >>
> >> >> After using pdb2gmx I receive this command:
> >> >>
> >> >> You have successfully generated a topology from: g3n.pdb
> >> >> The CA force field and the spce water model are used.
> >> >>
> >> >> Then I define box and solvent without any problems, but there are
> many
> >> >> errors when I execute grompp command as follows:
> >> >> Error 892 [file topol.top, line 6147]
> >> >> No default G96Angle types
> >> >>
> >> >> and
> >> >> Error 904 [file topol.top, line 6159]
> >> >> No default Proper Dih. types
> >> >>
> >> >> However, when I checked these lines I understood that
> >> >> 1- many of these bonds, angles, and dihedrals are related to atoms
> that
> >> >> are
> >> >> not connected to each other, or
> >> >> 2- I have defined the appropriate bond, angle, or dihedral, but I do
> not
> >> >> know why pdb2gmx didn't assign them.
> >> >>
> >> >> you can see all the files via
> >> >> https://www.dropbox.com/s/c8csnchfdahe016/4MEHR.zip?dl=0
> >> >>
> >> >>
> >> > Indeed, you have many missing interactions. This means you either have
> >> not
> >> > added all of the necessary interactions that you think you have, or
> your
> >> > connectivity is wrong. It could even be both. Just looking at the
> first
> >> > three residues, you have bonds between residues 1-2 and 1-3. pdb2gmx
> >> won't
> >> > support this; your .rtp files can only specify bonds between
> consecutive
> >> > residues via the +/- mechanism. So you're probably getting some
> >> unexpected
> >> > connectivity. I don't see any bond between atoms 1 and 27 as your
> first
> >> > message claimed. You may be able to get specbond.dat to work somehow
> >> here,
> >> > as that is the only way to assign bonds between non-consecutive
> residues.
> >> >
> >> > -Justin
> >> >
> >> >
> >> > Excuse me for my poor English,
> >> >>
> >> >> Truly yours,
> >> >> Farideh
> >> >>
> >> >> On Wed, Sep 30, 2015 at 3:03 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> >> >>
> >> >>
> >> >>>
> >> >>> On 9/30/15 7:21 AM, faride badalkhani wrote:
> >> >>>
> >> >>> Dear all,
> >> >>>>
> >> >>>> Could you tell me what is wrong when there are some strange bond,
> >> angles
> >> >>>> and dihedrals in the topology file after executing pdb2gmx command?
> >> >>>> for example atoms 1 and 27 do not have any connectivity, but
> pdb2gmx
> >> >>>> generate them as [bonds]. A similar problem occurs in case of
> angles
> >> and
> >> >>>> dihedrals.
> >> >>>>
> >> >>>>
> >> >>>> Impossible to say without knowing what you're actually doing.
> Please
> >> >>> always provide a full description of your system, your pdb2gmx
> command,
> >> >>> and
> >> >>> any relevant output, snippets of files, etc.
> >> >>>
> >> >>> -Justin
> >> >>>
> >> >>> --
> >> >>> ==================================================
> >> >>>
> >> >>> Justin A. Lemkul, Ph.D.
> >> >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >> >>>
> >> >>> Department of Pharmaceutical Sciences
> >> >>> School of Pharmacy
> >> >>> Health Sciences Facility II, Room 629
> >> >>> University of Maryland, Baltimore
> >> >>> 20 Penn St.
> >> >>> Baltimore, MD 21201
> >> >>>
> >> >>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> >>> http://mackerell.umaryland.edu/~jalemkul
> >> >>>
> >> >>> ==================================================
> >> >>> --
> >> >>> Gromacs Users mailing list
> >> >>>
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> >> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> >>> posting!
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> >> >>>
> >> >>>
> >> > --
> >> > ==================================================
> >> >
> >> > Justin A. Lemkul, Ph.D.
> >> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >> >
> >> > Department of Pharmaceutical Sciences
> >> > School of Pharmacy
> >> > Health Sciences Facility II, Room 629
> >> > University of Maryland, Baltimore
> >> > 20 Penn St.
> >> > Baltimore, MD 21201
> >> >
> >> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> > http://mackerell.umaryland.edu/~jalemkul
> >> >
> >> > ==================================================
> >> > --
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> >> --
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> >
> >
> >
> > --
> >
> > Chandan Kumar Choudhury
> > National Chemical Laboratory, Pune
> > India
> >
> > *"All work and no play makes Jack a dull boy...”*
> > --
> > Gromacs Users mailing list
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