Hi,<br><br>I am dealing with the lipid bilayer permeation simulation.<br>Most compounds can be finished, but the compounds with CN can't be performed simulation.<br>I have searched the discussion in the gmx-users discussion.<br>
The "vsite" has been mentioned, and I have refered to the gromacs manual.<br>But I don't understand that how I can use the "vsite".<br>(add the toplogy file or use the command line?)<br>I attach the PDB and toplogy file of the molecule.<br>
First, I performed the molecular dynamic simulation for the pure lipid bilayer, and the step was been finished.<br>After I insert the molecule, these command lines are performed.<br><br>grompp -f minim.mdp -c cmplx.pdb -p topol_dppc.top -o em.tpr<br>
mdrun -v -deffnm em<br>grompp -f npt_cmplx.mdp -c em.gro -p topol_dppc.top -o npt_cmplx.tpr<br>nohup mdrun -v -deffnm npt_cmplx &<br><br>Thanks for your help.<br>Best,<br><br> Chia-yun<br>