Hi, the function used by GROMACS is Vd (öijkl ) = kö (1 + cos(nö − ös )), for proper dihedrals (periodic type). Take a look at Chapter 4, of GROMACS-4-0 manual.
Antonia >prasun kumar <[email protected]> said: > --000e0cd20d869ab935046434ec49 > Content-Type: text/plain; charset=ISO-8859-1 > Content-Transfer-Encoding: 7bit > > Respected all > I drew the structure using the drawing tool available in PRODRG server > then I went for topology file generation,but the server is deleting almost > all the hydrogen atoms while writing the topology file for gromacs > can any one tell me why it is doing like this? > > another question I got that is > how to change gromacs topology file to charmm topology file > (I know for bond length and angle........but for dihedral(improper and > proper)) > actually i want toi know which function gromacs is using for the calculation > of dihedrals.......... > thanx in advance > > PRASUN (ASHOKA) > > --000e0cd20d869ab935046434ec49 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > > Respected all <br>I drew the structure using the drawing tool available in = > PRODRG server<br>then I went for=A0 topology file generation,but the server= > is deleting almost all the hydrogen atoms while writing the topology file = > for gromacs<br> > can any one tell me why it is doing like this?<br><br>another question I go= > t that is<br>how to change gromacs topology file to charmm topology file <b= > r>(I know for bond length and angle........but for dihedral(improper and pr= > oper))<br> > actually i want toi know which function gromacs is using for the calculatio= > n of dihedrals..........<br>thanx in advance<br><br clear=3D"all">PRASUN (A= > SHOKA)<br> > > --000e0cd20d869ab935046434ec49-- > -- _______________________________________________ gmx-users mailing list [email protected] http://www.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
