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
