From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Wed Nov 16 2011 - 15:12:17 CST
Dear NAMD experts,
I am planning to use "umbrella sampling" method in NAMD to obtain the PMF profile for the ion movement along channel.I found a useful link posted on NAMD mailing list which suggests to use "histogram" method inside the colvars module:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/12631.html
I have used "colvars" module before to run ABF simulations so I am familiar with it. I defined a "DistanceZ" colvar to move my ion along Z direction (dynamic axis) with respect to "rm". For the "umbrella sampling" part, I first defined a "harmonic" potential to keep the distance of ion fixed with respect to "rm". Then, I used "histogram" as below:
harmonic {
colvars AtomDistance
centers 1.00
forceConstant 10.0
}
histogram {
colvars AtomDistance
outputFreq 100
}
The only generated output files related to RC and force are ".traj" and ".dat". In the first one force and ion position along dynamic axis are reported during time and the only useful information from the second one is the number of samples in the bins. Is that what I am supposed to get? Are these output files enough to run "WHAM" or I am missing something here?
Is there any other way to put the windows together and obtain PMF profile rather than using "WHAM"? And finally, is there any command to run the windows together using one "umbrella sampling" simulation? Unlike ABF, I could not find any specific tutorial in NAMD to run umbrella sampling. Is there a specific tutorial for it?
Please let me know,
Parisa
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