about calculation of PMF from SMD trajectories

From: Falgun Shah (fhshah_at_olemiss.edu)
Date: Wed Mar 04 2009 - 11:58:52 CST

Dear NAMD users

I need your help regarding calculation of PMF with NAMD. I have performed
SMD simulation using NAMD (http://www.ks.uiuc.edu/Training/Tutorials/)
little different way then shown in deca alanine stretching tutorial for
computing PMF from deca alanine smd trajectories. i have attached
configuration file for your reference which i used for the calculation of
SMD for protein of my interest. i have all the trajectories with me. In the
tutorial for computing PMF in NAMD for deca alanine, the da_SMD_tcl.out file
is generated which has the information about the time, distance and applied
force. In my case, i have log file which has Time, components of the applied
force as well as the coordinates of the SMD atoms. However, i dont know how
should i implement this information to calculate work using the information
given in the tutorial. Also, the langvein dynamics was set to off during SMD
calculation in my case (please see the config file). does it have a
significant impact on the smd simulation? I have used spring force constant
of 5 kcal/mol/A and 0.02A/ps of constant velocity as shown in config file
for pulling out my ligand. Is this velocity is sufficient enough for
computing PMF. With this information available, how should i go ahead for
calculation of work as well as further average them according to jarzynksi's
averaging scheme (exponential average and 2nd order cumulant). is there any
scripts available for the extracting required information or Do i need to
re-run the SMD simulations as shown in the deca-alanine tutorial. I want to
calculate the PMF using the scripts mentioned in the tutorial. Please let me
know if any important parameters, i am missing in the configuration file
which might be crucial for the calculation of PMF. I would really appreciate
your reply. Thanks.

Falgun H shah
PhD candidate (3rd year)
Department of Medicinal Chemistry
2028, Natural Product Center
University of Mississippi
Ph No: 6629151286(O)
          662 801 5667(M)
email: fhshah_at_olemiss.edu

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