I have done SMD of protein at applying constant velocity using NAMD software and CHARMM ff. Since, this is my first time in performing Steered MD, I am not sure as to should I do umbrella sampling alongwith SMD? Are the results of SMD without any umbrella sampling significant ? It would be helpful if I could get some references as well.
Steered MD simulation is essentially Umbrella Sampling simulation if the velocity of pulling is very small. You can, however. combine steered md simulations with umbrella sampling . For example, you can use SMD, which is a non-equilibrium simulations, to generate different configurations of your systems, then use these configurations as starting point for the equilibrium umbrella sampling simulations, as shown in the following reference.
http://physique.umontreal.ca/~mousseau/articles/126.pdf
Thank you Kamberaj. Correct me if I am wrong I should do a short stretch of SMD first which will generate an output trajectory. From that I should take the final snapshot and perform Umbrella Sampling. Then the output of Umbrella Sampling is taken as input for SMD ??? Thanks
I also mentioned in another thread, Steered MD is essentially equivalent to Umbrella Sampling if the velocity of pulling is very small. There is an example of combining SMD with umbrella sampling technique on this link:
http://physique.umontreal.ca/~mousseau/articles/126.pdf
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