From: Q=AF=9B=E8=BF=90=E9=93=96?= (catmyc_at_gmail.com)
Date: Fri Aug 16 2013 - 13:28:05 CDT
Dear Mattew,
The count for ABF forces is accumulated and wouldn't start over when the system leaves and than return to this bin.
To confirm the convergence of ABF calculation, continuity of force is of course necessary. Besides, I advice that the ABF profile be documented repeatedly after a certain period.Then you can calculate the RMSD of the force profile with respect to a reference you've chosen. When the RMSD comes to a plateau, the ABF calculation can be regarded as converged.
Best regards!
Mao
-----原始邮件-----
发件人: "Matthew Ralph Adendorff" <mraden_at_mit.edu>
发送时间: 2013/8/14 0:40
收件人: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
主题: namd-l: Non-equilibrium effects in ABF runs
Good day,
I have a question regarding the fullSamples parameter for Adaptive Biasing Force runs. I am looking to run ABF on some DNA duplexes in explicit solvent and so am concerned about non-equilibrium effects in the runs. When the system enters a bin, the fullSamples parameter sets how many counts must be reached before the bias is applied to that bin. Let's say we have set fullSamples to 1000 (very small for this type of system I know). If the system were to move out of Bin A, after 1000 counts, into an adjacent Bin B under the influence of the bias and then move back into Bin A (perhaps through natural diffusion of the reaction coordinate), would another 1000 counts need to be achieved before more bias is applied? If this is the case, perhaps a blocking method could be used to determine the best value of fullSamples to ensure that the system is in fact equilibrated before more bias is added. If not, is there an effective way, perhaps through checking autocorrelation functions ove!
r time, to ensure that non-equilibrium effects have been accounted for in sampling along the reaction coordinate? I understand how to check when a trajectory has equilibrated, however, I am unsure as to whether a biased trajectory can be treated in a similar fashion as forces are continually being added to the simulation. Any advice/referral to extra reading would be greatly appreciated.
Best regards,
Matthew
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