Run simulation in NAMD using files generated by CHARMM-GUI

From: Dai, Jian1 (jian1.dai_at_ttu.edu)
Date: Tue Jun 01 2010 - 00:09:27 CDT

Hi, NAMD users:
We're trying to run DPPC bilayer simulation.
The 1st question: I basically followed the steps of membrane builder on CHARMM-GUI to get the psf file in X-PLOR format and the pdb file. However, when viewing the structure, the two hydrogen atoms of water molecules appear to be linked together. Checking the relevant psf file section indicates that there are bonds between these two hydrogens. Is this what's supposed to be? The two hydrogen atoms of water are not bonded together in membranes generated by the MEMBRANE plugin of VMD.
The 2nd question: I used scripts to extract only the DPPC bilayer, i.e., no water molecules and then solvate the pure DPPC with the SOLVATE plugin of VMD. When I tried to run the energy minimization, the simulation seems to be abnormal. The coordinates of atoms in the system hardly changes. The water molecules don't move. Can someone give us some suggestions?
The configuration file, psf and pdb files are available at:
http://rapidshare.com/files/393889353/em.conf
http://rapidshare.com/files/393889770/bilayer_sol.psf
http://rapidshare.com/files/393889957/bilayer_sol.pdb
Really appreciate any help.
Thank you.
Jian

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