[AMBER] Inquries about Non-periodic PMF profile

From: Meng Wu <wumeng.shanghaitech.edu.cn>
Date: Sat, 28 Jul 2018 14:26:37 +0000

Dear all,

    I was using WHAM to analyze the PMF profile for a channel transportation. However, the start (PMF = 0 Kcal/mol) and end points(PMF= 10 Kcal/mol) have different values instead of a periodic curve. I did the umbrella sampling with amber16 and refered the "AMBER-Umbrella_COM_restraint_tutorial"(https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial), and my WHAM command is: wham -25 25 8600 0.00000001 310 0 actdata.dat out.pmf. I firstly did the SMD to pull the substrate molecule which initially stays in the middle of the channel in up and down along the z direction separately, then 86 windows in total were extracted to do the restraint simulations.

    Could anybody give me some advice about this problem? Thank you in advance!

All the best,
Meng Wu

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Received on Sat Jul 28 2018 - 07:30:01 PDT
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