Hi, may I ask how do you get the potential energies from a simulation? Is it possible to get continuous energy-time graph for a system?
thanks in advance Jan Neumann David Mobley schrieb: > Maybe this is what someone is getting at in their answers, but you > COULD sort of "invert" the problem: Use mdrun -rerun to calculate the > energy of the system WITHOUT the dihedrals you are interested in (i.e. > by removing these). And then if you subtract the potential energies > for that from the original potential energies, you'll have the > dihedral potentials of interest. > > David > > > On 8/17/06, Bob Johnson <[EMAIL PROTECTED]> wrote: >> Hello everyone, >> I would like to measure the dihedral energy of certain portions of >> the same >> molecule over the course of a previously calculated trajectory. It's >> important >> that I get the energy of ONLY these portions. I thought of saving the >> trajectory of the portion in interest using trjconv. Then using mdrun >> -rerun to >> calculate the dihedral energy of this portion. However, this won't >> work because >> I would have to make a topology file that contains ONLY this portion. >> Any >> ideas? >> Bob >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> 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 >> > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
