Hi All I want to calculate the number of contacts between a small molecule and a oligonucleotide from a MD run. I read in the manual that in the itp file is possible, setting 2 for the combination rule within the section [ defaults ], to give sigma and epsilon instead of c6 and c12 LJ parameters. If I'm not wrong, the value of the interaction at the equilibrium point is -epsilon, so putting epsilon=1 for all but hydrogens atoms types in itp file, and setting a cutoff of 3.5 or 4 angstrom, re-running the trajectory with the proper groups in energy specifications, I should approximately get the number of contacts. Unfortunately this seems not to be the case, I get a number of contacts of one order of magnitude bigger than expected, but I do not understand what's going wrong...
There is something I'm missing or misunderstanding? Can anyone help me?!?!?!? Thanks in advance Attilio --------------- Attilio Vittorio Vargiu PhD in Biophysics at SISSA/ISAS via Beirut 2-4, Trieste (Italy) phone: 00390403787335 ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ _______________________________________________ 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
