Hello all I have a small query regarding neutralization of charges in vaccum simulations. I would like to simulate in vaccum 10 copies of 10 residue peptide containing one charged residue lysine (I am interested in monitoring cation-pi interactions between them).
1) Would you suggest me to neutralize the system (since electrostatic neutrality is required for the MD simulations of the system) even though I would like to monitor cation pi interactions? 2) How can I deal with the charges in-vaccum simulations? Since there are no solvent molecules with dipole, would the addition of salt ions be energetically be stable? 3)Also, I have read few papers in which MD simulations were carried out without neutralization of charges. Is it reasonable to carry out such simulations? Thanks in advance. -- View this message in context: http://gromacs.5086.x6.nabble.com/charges-in-vaccum-simulations-tp5014566.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
