[gmx-users] about -CN triple bond
Mark Abraham
mark.abraham at anu.edu.au
Mon Feb 28 12:31:29 CET 2011
On 02/28/11, "C.Y. Chang" <chiayun.chang at gmail.com> wrote:
> Hi,
>
> I try to add a dummy atom in my small molecular pdb and
> topology file. (attached files)
> But the MDS process still shut down.
> The msg. is
> [1]+ Exit 255 nohup mdrun -v -deffnm npt_cmplx
>
>
> Could you give me some suggestions for dealing with the problem.
>
Solving the problem requires removing the one of the three existing co-linear atoms by treating it as a virtual atom. You haven't done that. You've introduced a fourth co-linear atom - the dummy. Treat the central C atom as a dummy. That reduces your number of non-virtual co-linear atoms to 2 in all cases. That solves this problem.
Mark
>
> Thaks a lot.
> Best,
>
> Chia-yun Chang
>
>
>
>
> 2011/2/19 Mark Abraham <Mark.Abraham at anu.edu.au>
>
> >
> >
> >
> >
> >
> >
> >
> >
> > On 19/02/2011 5:18 PM, C.Y. Chang wrote:
> >
> >
> > > Hi,
> > >
> > >
> > >
> > > The errpr msg. that I expressed in the previous mail is unclear.
> > >
> > > It really happened in the grompp step of my dealinw with the em.
> > >
> > > The manual shows that the viste can be used by
> > >
> > >
> > >
> > > [ virtual sites2 ]
> > >
> > >
> > >
> >
> >
> >
> > That's misspelled too. Underscores are significant. You have to be
> > literal when dealing with computers.
> >
> >
> >
> >
> > >
> > > ; Site from funct a
> > >
> > > 5 1 2 1 0.7439756
> > >
> > >
> > >
> > > What should I choose the vsite for the -CN group? (2, 3fd or
> > > others?)
> > >
> > >
> >
> >
> >
> >
> > The problems come when the force from normal angle and dihedral
> > functions aren't numerically stable when there are 3 collinear
> > atoms. The way to avoid this is to have one of those atoms
> > "virtual". Forces on it get projected onto the real atoms from which
> > it is defined, the integration of forces proceeds only on the real
> > atoms, and the position of the virtual site gets reconstructed
> > later. So, which type do you think will work best here?
> >
> >
> >
> >
> > > I read the manual and the columns of the vsite need
> > > some parameters.
> > >
> > > The "Site" seems to be the atom number.
> > >
> > >
> >
> >
> >
> >
> > Yes.
> >
> >
> >
> >
> > >
> > > The "from" seems some atom group, but which atoms should be
> > > included?
> > >
> > >
> >
> >
> >
> >
> > The real atoms that form the virtual site. The number and order
> > depends on the type of virtual site. Which atom is which is covered
> > back in 4.7 You need to read that together with 5.2.2, like I said
> > several emails ago.
> >
> >
> >
> >
> > > How could obtain the "func" values?
> > >
> > >
> >
> >
> >
> >
> > That's situation-dependent. Here, you want to pick a position along
> > the line that will lead to the three atoms being a sensible distance
> > apart.
> >
> >
> >
> >
> > > Could you give me a molecule for my example?
> > >
> > >
> >
> >
> >
> >
> > No, I don't have one. Your example above will construct atom 5 from
> > 1 and 2 75% of the way along the line from 1 to 2, per Figure 4.16
> > and equation 4.134.
> >
> >
> >
> > Mark
> >
> >
> >
> >
> >
> > > Thanks for your help.
> > >
> > >
> > >
> > > Best,
> > >
> > >
> > >
> > > Chia-yun
> > >
> > >
> > >
> > >
> > >
> > > 2011/2/19 Mark Abraham <Mark.Abraham at anu.edu.au>
> > >
> > >
> > > >
> > > >
> > > > On 19/02/2011 3:02 PM, C.Y. Chang wrote:
> > > >
> > > >
> > > > > Hi,
> > > > >
> > > > >
> > > > >
> > > > > I have tried to add
> > > > >
> > > > >
> > > > >
> > > > > [ position restraints ]
> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > > > This is misspelled. Surely grompp warned about this?
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > > 2 1 1000 1000 1000 ; Restrain to a
> > > > > point
> > > > >
> > > > > 1 1 1000 0 1000 ; Restrain to a line (Y-axis)
> > > > >
> > > > > 3 1 1000 0 0 ; Restrain to a plane (Y-Z-plane)
> > > > >
> > > > >
> > > > >
> > > > > in the end of the topology file.
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > This does not even approach the solution to your problem.
> > > > Position restraints inhibit diffusion and structural
> > > > changes. You need a vsite, like you knew earlier.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > > In the em. process, I get the
> > > > > eroor msg.
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > No, this error happened in grompp.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > > Fatal error:
> > > > >
> > > > > Invalid dihedral type 1000
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > GROMACS didn't recognise the mis-spelled directive, and so
> > > > it's trying to make sense of your position restraint lines
> > > > as dihedrals.
> > > >
> > > >
> > > >
> > > > Mark
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > >
> > > > > Chia-yun
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > 2011/2/18 Mark Abraham <Mark.Abraham at anu.edu.au>
> > > > >
> > > > >
> > > > > >
> > > > > > On 18/02/2011 1:13 PM, C.Y. Chang wrote:
> > > > > >
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > I am dealing with the lipid bilayer permeation
> > > > > > > simulation.
> > > > > > >
> > > > > > > Most compounds can be finished, but the
> > > > > > > compounds with CN can't be performed
> > > > > > > simulation.
> > > > > > >
> > > > > > > I have searched the discussion in the
> > > > > > > gmx-users discussion.
> > > > > > >
> > > > > > > The "vsite" has been mentioned, and I have
> > > > > > > refered to the gromacs manual.
> > > > > > >
> > > > > > > But I don't understand that how I can use the
> > > > > > > "vsite".
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > The theory is discussed in chapter 4 and there's a
> > > > > > brief example in 5.2.2. What have you tried and
> > > > > > what went wrong?
> > > > > >
> > > > > >
> > > > > >
> > > > > > Mark
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > >
> > > > > > > (add the toplogy file or use the command
> > > > > > > line?)
> > > > > > >
> > > > > > > I attach the PDB and toplogy file of the
> > > > > > > molecule.
> > > > > > >
> > > > > > > First, I performed the molecular dynamic
> > > > > > > simulation for the pure lipid bilayer, and
> > > > > > > the step was been finished.
> > > > > > >
> > > > > > > After I insert the molecule, these command
> > > > > > > lines are performed.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > grompp -f minim.mdp -c cmplx.pdb -p
> > > > > > > topol_dppc.top -o em.tpr
> > > > > > >
> > > > > > > mdrun -v -deffnm em
> > > > > > >
> > > > > > > grompp -f npt_cmplx.mdp -c em.gro -p
> > > > > > > topol_dppc.top -o npt_cmplx.tpr
> > > > > > >
> > > > > > > nohup mdrun -v -deffnm npt_cmplx &
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > Thanks for your help.
> > > > > > >
> > > > > > > Best,
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > Chia-yun
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > >
> > > > > > gmx-users mailing list gmx-users at gromacs.org
> > > > > >
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> > > > > >
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> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > >
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> >
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