On 02/28/11, "C.Y. Chang" <chiayun.ch...@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.abra...@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.abra...@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.abra...@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@gromacs.org > > > > > > > > > > > > > > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > > > > > > > > Please search the archive at > > > > > > http://www.gromacs.org/Support/Mailing_Lists/Search > > > > > > before posting! > > > > > > > > > > > > Please don't post (un)subscribe requests to > > > > > > the > > > > > > list. Use the www interface or send it to > > > > > > gmx-users-requ...@gromacs.org. > > > > > > > > > > > > Can't post? Read > > > > > > http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > gmx-users mailing list gmx-users@gromacs.org > > > > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > > > > Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/Search > > > > before posting! > > > > > > > > Please don't post (un)subscribe requests to the list. Use the > > > > > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > > > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > gmx-users mailing list gmx-users@gromacs.org > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > Please don't post (un)subscribe requests to the list. Use the > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > >
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