[gmx-users] gromacs 4.5.4 analysis tools

2011-04-03 Thread Molecular Dynamics
Dear gmx users, I’m a NAMD user and want to use gromacs 4.5.4 analysis tools for my NAMD output files. I have some NAMD output files : output.coor , output.vel , output.dcd (binary coordinate trajectory output file). Can I convert these output files into gromacs output files and use gromacs 4.5.

[gmx-users] make_ndx and rdf

2011-10-03 Thread Molecular Dynamics
Dear All, I want to calculate rdf for carbon-oxygen, carbon-hydrogen and carbon-water using g_rdf but how can I generate an .ndx file that are suitable for these systems ? I searched mailing list and read manual but couldn't generate .ndx file using make_ndx tool. However, I tried to see the ma

[gmx-users] n-alkanes simulations in Gromacs

2009-02-28 Thread Molecular Dynamics
Dear Gromacs Users, I’m interested in  n-alkanes and  evaluating thermophysical and structural properties of n- alkanes  and  binary mixtures  of n-alkanes. I want to use Gromacs and the force fields in Gromacs for my n-alkanes simulations. And I want to ask some questions to you. First, I’m pla

[gmx-users] using more than one type of molecules

2009-03-13 Thread Molecular Dynamics
Dear All, I'm new to Gromacs and have some questions to learn the answers. I study on one type molecule. If I want to add lets say 240 molecules, which is the best way to use editconf or genbox ? And I learned the procedure of using more t

Re: [gmx-users] using more than one type of molecules

2009-03-14 Thread Molecular Dynamics
___ From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Friday, March 13, 2009 8:25:14 PM Subject: Re: [gmx-users] using more than one type of molecules Molecular Dynamics wrote: > > > Dear All, > > > I'm new to Gromacs and have some questions t