Sorry for insisting, but has no-one any idea of this....? Thanks
Juan José Galano Frutos Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, University of Zaragoza Pedro Cerbuna # 12, 50009 Zaragoza (Spain) +34 976 76 28 06 Institute for Biocomputation and Physics of Complex Systems (BIFI) Mariano Esquillor, Edificio I + D - 50018 Zaragoza (Spain) ---------- Forwarded message ---------- From: Juan José Galano Frutos <juanj...@gmail.com> Date: 2017-03-20 14:34 GMT+01:00 Subject: NORMAL MODES analysis to compute specific heats To: gmx-us...@gromacs.org Hi there: I've been googled a bit about this issue (http://thread.gmane.org/ gmane.science.biology.gromacs.user/49139, http://www.gromacs.org/ Documentation/How-tos/Normal_Mode_Analysis, https://groups.google.com/ forum/#!topic/archive-gmx-users/5C5Q8m9X21g), but I've not found answers to my doubts yet. My situation is that I want to obtain specific heats (Cp) of my systems (protein solvated and neutralized) but, of course, at the Temperature and Pressure of my experiments. So, my idea here is carry out a Normal Modes analysis to extract the Hessian matrix but at least after the equilibration step of my system. I'm interested in doing it so because Cp values only make sense in relation with Temperature. My doubts come up, however, when I read through the posted discussion and I find that NM analyses apparently should be performed after minimization steps (Conjugate gradient and/or L-BFGS). Then, I would like to ask you if that is really so or if it is possible carry out this calculation after, for instance, an equilibration or a productive step in which, of course, some previous minimizations have already been performed as usual? I've not understood also the suggestion made in one of the above referenced discussions in which David Van der Spoel recommended set all cut-offs to zero (=infinite), see below: > You can use the g96 coordinate format instead of using the trr file > from the conjugate gradients energy minimization. > Set all cut-offs to zero (= infinite). What's the reason for that? Where one should set to zero the cut-offs...? Just in the NM step or that is for the minimization steps? Thank you very much for your help. Juan José Galano Frutos Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, University of Zaragoza Pedro Cerbuna # 12, 50009 Zaragoza (Spain) +34 976 76 28 06 <+34%20976%2076%2028%2006> Institute for Biocomputation and Physics of Complex Systems (BIFI) Mariano Esquillor, Edificio I + D - 50018 Zaragoza (Spain) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
