TOTLAL2, POTENTIAL abd aMD

From: sunyeping (sunyeping_at_aliyun.com)
Date: Mon Sep 30 2013 - 03:11:43 CDT

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Dear all,        I am trying to use the accelerated MD with NAMD, and I am not sure how to define the parameter accelME (Threshold energy E) and alpha. I have a previous run of normal MD whose output log file contains the POTENTIAL values. Should I extract these POTENTIAL values of all steps from this MD run and get a average and set accelME a little higher than it? If so, how should I extrat the POTEINTIAL values. In VMD, the NAMDplot funtion can extract TOTAL, TOTAL2, and TOTAL3, but there is no TOTAL2 in my MD output. Is TOTAL2 equal to POTENTIAL in my MD output? And how can I extract POTENTIAL values? Best Regards, Yeping Sun Institute of Microbiology, Chinese Academy of Sciences

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