Hi,
Thanks in advance for your help.
I tried using the command g_energy to get xvg files that can be in turn used for plotting graphs using xmgrace but I am getting the following error:
Used command: g_energy -f md_0_1.edr -n index.ndx -o pres.xvg
Error: g_energy: command not found
Do I need to install or copy a script for this command to work? Or am I missing something?
I think you need to give the full path of the g_energy program.
In case you are using Gromacs 5.0 or higher, use gmx energy command.
@Swapnil Thanks for your reply.
I need a little more info. When using gmx energy which .edr file should be given as input?
1. output of NVT equilibrium step
2. output of NPT equilibrium step
3. output of production step
I tried using all the 3 mentioned using the command given below:
gmx energy -f md_0_1.edr -o energy.xvg
It gives me an error as:
File input/output error:
energy.xvg
What could be the possible reason for this?
Manasa, you need to use the production step .edr file if you wish to know the results of your simulation. However checking energy during equilibrium will only give you an idea whether your system is well equilbrated.
Vinayak, so to check if the system is well equilbrated, we should use NVT/NPT edr files right? When I am using those files why is it throwing an input/output error? Should I input anymore files besides .edr files?
gmx energy -h will display the details of the energy tool. Only .edr is required. While others are optional. Try giving the location to your .edr file. Maybe you don't have permissions to write a file your working directory.
Manasa:
1. For equilibration you need to plot the energies for NPT/NVT simulations. For MD run, it will be md_0_1.edr
2. Make sure you put ab output option for energy in your mdp file.
3. From the command line you said you entered, it seems like you din't put a space beteween md_0_1.edr and -o; make sure you put a space.
And ultimately gmx energy -h is there to help you out :)
for performing npt equilibriation, the command
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
it says in the next step that .edp file does not exist or accessible.
can anybody help?
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