I am trying to use the gmx energy model to make free energy calculations upon binding of a ligand to a receptor. To do this I am invoking the energy module and adding the -odh flag:
gmx energy -f md_0_1.edr -s md_0_1.tpr -odh
This returns an error saying:
Fatal error:
No dH data in md_0_1.edr
I have looked into this and can see it is possible to include dH data using the -dhdl flag in gmx mdrun. I have tried including this flag during the production MD stage like so:
gmx mdrun -deffnm md_0_1 -dhdl
However I still get the same fatal error.
Does anyone know how to store dH data into the .edr file?
Hi Oliver! Please, read official manual for gromacs software. Basically, it is mentioned there that you shall specify the name of the output xvg-file after -dhdl flag. http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-mdrun.html
Inna Ermilova Hi, thanks for the response. I'm afraid I did try that as well:
gmx mdrun -deffnm md_0_1 -dhdl dhdl.xvg
However, no dhdl.xvg file was generated in the output. In any event, the gmx energy module seems to require the dH information is stored in the .edr file rather than a separate xvg.
Any thoughts?
Hi again, Oliver! Then I assume you have made some mistakes when you were trying to create lambda points for the free energy calculation. So if you are really trying to set up the free energy calculation then this tutorial will be useful. (http://www.gromacs.org/@api/deki/files/262/=gromacs-free-energy-tutorial.pdf ) Download files, mentioned in the pdf-document (click on the link after wget). Check scripts and other files, then, hopefully, you can fix your calulation.
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