On Wed, 1 Nov 2006, Attilio Vargiu wrote: >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?!?!?!? >
you are mixiing things up. calculating the number of contact is done after a simulation using an analysis tool (g_mindist -on). This has nothing to do with simulation settings, topoogies etc. >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 > -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ 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
