> Hi All, > > I meet a problem in run MD: from the display of VMD, there are some H-H > bonds formed during the MD. All the bonds I wrote in .itp file are right, > except these new unexpected H-H bonds. (I generate the system from a > smaller system, EM is ok, when running NTV, the problem comes. ) Who can > give some suggestions? Thanks in advances.
Unless you opened the structure from a .tpr file, VMD can't even have accessed your topology. It has its own heuristics for deciding whether to show a bond exists. See the VMD documentation for details. Whether these close H-H contacts are a problem is for you to judge :-) Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
