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
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 hav
Hi,
I have tried to add
[ position restraints ]
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.
In the em. process, I get the eroor msg.
Fatal error:
Invalid dihedral type 100
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
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 ]
; Site from funct a
5 1 2 1 0.7439756
What should I choose the vsite for the -CN group? (2, 3fd
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.
Hi,
I added these words in the end of the topolgy
[ virtual_sites2 ]
; Site from funct a
5 1 2 1 0.7439756
and changed the mass of the atom 5 to zero.
When I performed the grompp before the MDS, it showed some error msg.
Reading position restraint coords from em.gro
Cleaning up constraints and
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 255nohup mdrun -v -deffnm npt_cmplx
Could you give me some suggestions for dealing with the problem.
Thaks a lot.
Best,
On 02/28/11, "C.Y. Chang" 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 suggestion
Hi,
I have modified the dummy atom in the topology (attached files) and pdb
file.
On the other side, I study the lipid system.
Therefore, I constrained all bond lengths in my system.
This is bond parameters in the mdp file.
continuation= no; starting up
constraints = all-bonds
On 1/03/2011 4:58 PM, C.Y. Chang wrote:
Hi,
I have modified the dummy atom in the topology (attached files) and
pdb file.
On the other side, I study the lipid system.
Therefore, I constrained all bond lengths in my system.
This is bond parameters in the mdp file.
continuation= no
Mark Abraham wrote:
On 1/03/2011 4:58 PM, C.Y. Chang wrote:
Hi,
I have modified the dummy atom in the topology (attached files) and
pdb file.
On the other side, I study the lipid system.
Therefore, I constrained all bond lengths in my system.
This is bond parameters in the mdp file.
cont
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