From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Fri May 04 2012 - 09:20:17 CDT
Dear NAMD experts,
I have been trying to use Umbrella Sampling (US) method to get the PMF profile in a channel. I have already obtained the PMF profile using ABF method and know how the profile looks like.
In US, I know that the first thing to check is the overlap between adjacent windows. Then, I followed all the instructions given in:
and I got a close PMF profile to ABF. In ABF I could check the force and sampling during time from history files to check the convergence. In US also I can generate PMF profiles during simulation to compare them during time. I am wondering what else I should check here? That is, as long as the overlap is enough and the harmonic potential is enough to keep the ions at the center of bin and the PMF profiles are not changing anymore during time, I should get a good and reliable profile? Is there anything else I should check?
Thanks in advance for your help,
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