[gmx-users] Energy Calculation

Hi! I want to calculate energy from GROMOS96-GB/SA. What command should be used? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe

[gmx-users] Normal mode analysis of pure water

Hi Berk, I want to determine the vibrational frequencies of water (close to the experimentally observed values for the three modes). And then extend the analogy for more complex systems. ___ gmx-users mailing listgmx-users@gromacs.org htt

[gmx-users] Normal mode analysis of pure water

Hi Justin, Are you suggesting that after thorough energy minimization, seperate .mdp file is to be used for NMA? In that case how would that output file (energy minimised file) be taken as an input file for the grompp and mdrun command (for NMA)? What extension would the file have

[gmx-users] Normal mode analysis of pure water

Hi Berk, You mentioned that standard NMA techniques will not work for the liquid water system. Could you suggest the alternatives then? ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users P

[gmx-users] Normal mode analysis of pure water

Hi Justin, I tried altering the .mdp file (integrator = steep instead of nm) for energy minimization. But in that case the mdrun did not generate the Hessian matrix (nm.mtx) inspite of using the command twice. ___ gmx-users mailin

[gmx-users] Normal mode analysis of pure water

Hi, I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution. mdrun_d -v -s water.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log -mtx nm.mtx Getting Loaded... Reading file water.tpr, VERSION 4.0.4 (double precision) Loaded with

[gmx-users] multiple T-Coupling groups

Hi, I used the followng command and encountered an error. Can someone please offer a solution. grompp -f grompp.mdp -n index.ndx -p topl.top -c conf.gro -o water.tpr :-) G R O M A C S (-: Green Red Orange Magenta Azure Cyan Skyblue

[gmx-users] how to create topology file for butane

Respected sir, I am working on GROMACS. I need your help.I am trying to generate topology file for non-standard molecules like butane, water. I am executing following command. *pdb2gmx -f ALA.pdb -p ALA.top -o ALA.gro* ** It is successfully working on amino acid residue.

[gmx-users] Normal mode analysis

Hi! I am a user of gromacs. Could someone provide me with a method (or set of commands) for normal mode analysis of small molecules (water, n-butane, etc). Also could you please provide a command for generating Hessian Matrix after the energy minimization. _