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". (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
1.pdb
Description: Protein Databank data
1.itp
Description: Binary data
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
