Thaks a lot.
Best,
Chia-yun Chang
2011/2/19 Mark Abraham <mark.abra...@anu.edu.au
<mailto: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
<mailto: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
<mailto: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
<mailto: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
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
<mailto: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
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
<mailto: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
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
