Dear all, I have been successfully using Gromacs for a couple years without bothering you - manual + reading the mailing list was completely enough.
But … this is the second mail for this afternoon. The question is: are there any analysis programs in GROMACS package which are sensitive to Periodic Boundary Conditions or they remove the periodicity automatically? Now I explain in more details what I mean: Let’s suppose that I have a trajectory file after some MD run with PBC. No shuffling, sorting and other things like that – only PBC. Then I am going to analyze the trajectory with g_rama, g_hbond, g_rdf, g_gyrate and, very probably, something else. Should I remove the periodicity first or I will be able to analyze the trajectory without bothering myself about that issue? I have already tried to analyze the PBC runs with and without removal of periodicity– the results are the same. But may be this is only due to the fact that my molecule didn’t move too much during the run and was placed as a whole in the periodic cell? And, in a general case I have to remove the periodicity to be 100% in the result of analysis. Sorry, for this, probably, silly question, but I am starting several series of simulations - I will be not physically able to check every time several hundreds of trajectories with or without periodicity removal (even with modern scripting languages a human being should take a look on the final results, isn't it :-)). With kindest regards, Maxim. Maxim V. Fedorov Research Associate. _______________________________________________ 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
