Dear all,
This is regarding the Steered Molecular Dynamics. After finishing SMD, extracted useful frames from the SMD trajectory and performed the brief NPT equilibration of the selected useful frame. These all new equilibrated frame considered for the short 10 ns MD run, but, I am not able to get the “pullf.xvg” and “pullf.xvg” file while performing the MD run.
As it is known or even explained in details in the Gromacs tutorial (http://www.mdtutorials.com/gmx/umbrella/07_analysis.html) that these *.xvg file is important to get the potential of mean force (PMF) or free energy using “wham module of Gromacs”.
Therefore, I would like to ask your suggestion for so. Why am I not getting the “pullf.xvg” and “pullf.xvg” file while performing the MD run of aforementioned equilibrated frames? It would be great if you could help me or give advice for so.
Thank You in advance
Nandan Kumar
The SMD module in gromacs is not very good according to my experience. I suggest you to use the PLUMED patch if you insist using gromacs. If you do not have a package preference, other MD programs such as AMBER, NAMD... are also good choices.
Hi Nandan,
I think you are not creating properly the tpr-files.dat -if pullf-files.dat, check these files contain the information needed to run gmx wham.
- Badges
- Science topic