Yes, the system is only POPC and water.
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com> Cc: Sent: Saturday, October 6, 2012 6:07 PM Subject: Re: [gmx-users] Model of water On 10/6/12 10:32 AM, Shima Arasteh wrote: > OK. > I did as follow as I described, but there is an error: > 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic > 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top > > Then added #include "charmm36.ff/tip3p.itp" to topol.top > > 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr > Fatal error: > number of coordinates in coordinate file (popc-solv.gro, 74672) > does not match topology (topol.top, 104936) > I checked the water molecules of popc-solv.gro by grep command ; > > # grep -c HW popc-solv.gro > 48696 > > > [ molecules ] > ; Compound #mols > POPC 238 > SOL 24348 > > > > What is the problem? would you please help me? I think the SOL molecule are > counted twice!! > You're off by a huge amount of atoms, so something is very wrong. The water molecules do not appear to be the problem. The number of HW/2 is equal to the number of SOL molecules. Is the system only POPC in water? No protein or any other components? -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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