Hi Callum,
Thanks for your kindly help! My channel protein is not symmetric, so I divided the whole SMD into two parts, the up-direction part and down-direction part along z axis, what's more, I rotated the down-part windows with negative z-valus just as the web tutorial suggested. After all the windows finished running, I manually added a minus sign in front of the distance column vales for the down-part windows which original in negative z-valus (Right or not?). When I put all the distance data files together and use WHAM to calculate the PMF, the problem that the previous mail said appeared. I think this is the "wrong" result because the substrate molecules are pulled into the water environment at both ends of the channel and the start & end points of the PMF file should be nearly zero. I personally think this is the non-periodic problem of WHAM, I have read the WHAM manual but it does not give the periodic information about distance(just angle). I have tried each window of 10ns and 20ns, the PMF curve converged
nearly in the same place, the difference is the size of the peak.
Here I read a paper about g_wham in gromacs (
https://pubs.acs.org/doi/abs/10.1021/ct100494z), it has the periodic option(-cycl). I am trying to use g_wham but the file format between amber and gromacs is a big problem...!
All the best,
Meng Wu
------------------------------
Message: 12
Date: Mon, 30 Jul 2018 18:39:10 +0000
From: "Dickson, Callum" <callum.dickson.novartis.com>
Subject: Re: [AMBER] Inquries about Non-periodic PMF profile
To: "amber.ambermd.org" <amber.ambermd.org>
Message-ID:
<423761a97f584c8f90e792d7b76af9fe.SN1PR6207MB0080.023d.mgd.msft.net>
Content-Type: text/plain; charset="gb2312"
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?
Best,
Callum
________________________________
From: Meng Wu <wumeng.shanghaitech.edu.cn>
Sent: Sunday, July 29, 2018 9:54:15 PM
To: amber.ambermd.org
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
________________________________________
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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_callumjd_AMBER-2DUmbrella-5FCOM-5Frestraint-5Ftutorial&d=DwIGbw&c=ZbgFmJjg4pdtrnL2HUJUDw&r=HwsFjSfOtLupDR-NuCP430rdz1DD2LkJxNM3BsKSjrw&m=wS5x5PZtujwGH6F5MkQam_1sghvv0l_nQZyzNmxW8iw&s=aMCFDkfz5g6ui4LXNy-SbqjhwCtsKB22Uqkv10OQ-5I&e=), 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 - 19:00:01 PDT
