On 9/11/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > Frankie Montenegro wrote: > > Hi again guys, > > > > Few more questions: > > > > 1. I would like to calculate compressibility of the protein+water > > system, but separating it into bulk water, hydration water and > > protein. So I need to pick these and compute volumes separately. When > > picking hydration water molecules, two tools are mentioned on the > > List: trjorder and g_hbond. Which one would you recommend for my task? > > Don't know, but I'd start by reading the man pages for each of those tools. >
I did that. They both seem OK to me. I am not that experienced with Gromacs though, which is why I'm asking for suggestion. > > 2. a)The program g_energy gives output for compressibility. What > > method was used for that calculation? > > See the manual first. > Did that too. Didn't find anything. I suppose I could go through the code. > > b) When running g_energy I noticed a particularly crappy number for > > the specific heat of SPC water with ffgmx forcefield. It is about > > 17J/mol.K (should be about 75). > > I get similar number with my code using energy fluctuation method. > > Do you guys have any suggestions? I cut and paste my equilibration and > > production run mdp files. > > Why are you generating velocities post-equilibration? > Upps! Thanks. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
