Hello, you can use for example Curves (Nucleic Acids Research, 2009, Vol. 37, No. 17 5917-5929) or 3DNA (http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html) to calculate them from any trajectory, I did but never used gromacs for this, I don't know if it is possible.
Hope this helps, Best Attilio 2010/6/8 shahab shariati <[email protected]> Hi gromacs users I want to simulate pr-dna by gromacs.I read a article (Biophysical Journal 87(6) 37993813) inwhich helical parameters for DNA (rise, slide, twist, roll, tilt, shift) calculated by md simulation, but I did not understand two things: How and what command these parameters were calculated? I read gromacs manual. in that there is only g helix and g helixorient for Protein specific analysis. can any body help me how to do this ? -- 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 ¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤ Attilio Vittorio Vargiu, PhD SLACS & Department of Physics, University of Cagliari Cittadella Universitaria S.P. Monserrato-Sestu Km 0.700 09042 Monserrato (CA), Italy e-mail1: [email protected] e-mail2: [email protected] Phone: +390706754847 Fax: +39070510171 ¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤¤ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ -- 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
