Thanks Justin for the advice and help, So i have to add in the bonded.itp O_2 C_2 CT OH with the parameters? or in the topology file (molecule) , y define the dihedral like OH CT C_2 O_2 ???
Thanks in advance Andres Ortega > Date: Sat, 1 Mar 2014 18:11:31 -0500 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] dihedral doubt > > > > On 3/1/14, 6:06 PM, Andres Ortega wrote: > > Hy Dear Gromacs Users, i have a question , > > i´m preparing a topolgy, but i need a dihedral > > i need O_2 C_2 CT OH, i could find it, > > but i find OH CT C_2 O_2 , i know that the order oof i j k l, is not the > > same, but there a way to use it > > > > i think that if i do this , is a big mistake.. > > > > Why? > > > can you help with this doubt ? > > > > Reversing the list of atom types is not a problem; it's rotation about the > same > bond so the parameters are the same. Confirm that the proper parameters have > been applied by using gmxdump on your .tpr file. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > [email protected] | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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 [email protected]. -- 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 [email protected].
