I am doing SMD of protein using NAMD and CHARMM ff. I have an output file which gives the 3 components of force applied and coordinates of the atom on which force is applied for various snapshots. I am somewhat confused about how to proceed calculating Potential of Mean Force.
You should have a look at this paper, where it is explained how to reconstruct the PMF from the trajectories obtained using SMD simulations:
Justin R Gullingsrud, Rosemary Braun, Klaus Schulten, Journal of Computational Physics, 151, 190, 1999.
Shaghayegh, I am sorry I am not exactly sure of what is going on. I am new in his SMD field. What I know of now is that I have attached the spring to the last residue of protein and pulling it keep the 1st residue fixed. The pulling is done along a vector that has an equal projection along the x and y coordinates and no projection along z. Actually I have followed the procedure give in this link http://www4.ncsu.edu/~franzen/public_html/CH795N/projects/SMD.htm. From the data I have got till now I could plot the Force vs extension curve (extension being distance between 1st and last residue). I have no clue as to how should I proceed or what I am doing is correct or not. Your hep in this regard is highly appreciated.
Thank you very much Shaghayegh for your response. I wouldlike to explain to you in details what I am doing so that you can help me a bit more.
After I did the SMD run, I am gettng an outputfile which gives the Fx,Fy,Fz (components of force) and coordinates (x,y,z) of the centre of mass of molcule which is being pulled for each snapshot. Right now I am not doing any umrella Sampling as I have kept my pulling velocity very low.
I have till now only plotted the Force vs extension curve, i.e., for each snapshot I calculated net force applied and extension (i.e., distance between centre of mass of first and last residue).
So, now I have vel, spring constant, net force (calculated from components of force) for each snapshot and coordinates of centre of mass (that is pulled) for each snapshot. I am really not sure how to calculate the PMF from these data. I would be really grateful if you could help me and take the pain in explaining the process of calculation in details.
Hundreds of SMD simulations can give you the free energy estimate e.g. using the Jarzynski equality... For instance, umbrella sampling (US), REUS can give you the PMF - the free energy along the specified reaction coordinate. There is a good tutorial of US by Justin Lemkul: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
The first few chapters of Frenkel Smit book on molecular simulation would help a lot. Time spent understanding the concepts will help you a lot later, and reading tutorials
given suggested above will help you apply what you have learnt. If instead you rush in and just apply the codes, you could have serious problems later.
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