[gmx-users] clustering and representative structure

Hi all, How are you? In Gromacs, the clustering methods are: o Full linkage o Jarvis Patrick o Monte Carlo o Diagonalization, and o Gromos what is the most cited method? what option generate "the most representative structure"? all the strategies? why? (not the average ge

[gmx-users]

Hi, I have two simple questions, o is possible to make MDs of poly-saccharides with the Gromacs software? o If yes, what force field have the appropriate parameters? only one FF? Thanks, Carlos Javier ___ gmx-users mailing listgmx-users@groma

Re: [gmx-users] Free energy calculations

Hi, the review by David Pearlman can be very useful in relation to FEP-type calculations o Free Energy Calculations: Methods for Estimating Ligand Binding Affinities Chapter 2 In: Free energy calculations in rational drug design M. Rami Reddy & Mark D. Erion Eds. Best regards, Javier N. Viswa

Re: [gmx-users] problems in installing fftw-3.0.1 under cygwin

Hi, Wilfred and Mark, thank you very much for the tips and your time. Best regards, Javier Nuñez -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.405 / Virus Database: 268.12.3/447 - Release Date: 9/13/2006 ___ g

[gmx-users] problems in installing fftw-3.0.1 under cygwin

Hi gmx-users, I am trying to install gmx-3.3.1 in my laptop (os windows xp & cygwin). Unfortunately, I didn't succeed to reproduce the instructions given by Mark Abraham in April-06. In my first attempt I uninstall (erroneously?) the fftw3 & fftw3-dev packages using the Cygwin installer. Whe