Hi, Justin. Thank you for your help! I was intended to reply the third question after I retryed the simulation under your advice,but I haven't enough time to do it. It's too late :)
Just now, I do a simulation. All seems ok. I will check it again. Thank you again! Cun Zhang > >pymol b4em.pdb # I write a python script to remove the SOL molecules > > in the Carbon nanotube. > > Are there any solvent molecules interfering with the cross-boundary bonds? > No.I use pymol to remove all residues which is far from the egdes 0.7A . > > >editconf -f b4em.pdb -o b4em.gro -box 3.8 3.8 5.614 #rebuild the box. > > Why are you doing this? > The b4em.pdb generated by genbox have no information about box size. So I use editconf to generate it. > NOTE 1 [file CNT.top, line unknown]: > > The largest charge group contains 32 atoms. > > Since atoms only see each other when the centers of geometry of the > charge > > groups they belong to are within the cut-off distance, too large charge > > groups can lead to serious cut-off artifacts. > > For efficiency and accuracy, charge group should consist of a few > atoms. > > For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. > > > > Pay attention to this note. A charge group of 32 atoms is huge. > So what's your suggestion about the number of a charge group? -- Blog: http://blog.4message.net
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
