Re: [AMBER] Inquries about Non-periodic PMF profile

From: Dickson, Callum <>
Date: Mon, 30 Jul 2018 18:39:10 +0000

Hi Meng,

Why is this the "wrong" result? Is the channel (and your membrane) symmetric? How long is each window and how does the PMF curve converge by extending the simulation time of each window?



From: Meng Wu <>
Sent: Sunday, July 29, 2018 9:54:15 PM
Subject: [AMBER] Inquries about Non-periodic PMF profile

Since maybe my last e-mail has been ignored, forgive me send it again. Could anybody give me some suggestions?

Best regards,
Meng Wu
发件人: Meng Wu
发送时间: 2018年7月28日 22:26
主题: Inquries about Non-periodic PMF profile

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"(, 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 Mon Jul 30 2018 - 12:00:03 PDT
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