Re: Multi canonical ensemble method

From: Takeru KAMEDA (kamedapon_at_hiroshima-u.ac.jp)
Date: Wed Nov 27 2019 - 00:19:06 CST

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Dear Giacomo.

Thank you for your kind reply, and sorry for the late response.

Almostly, I was able to perform ABF well because your attached URL included familiar information.

I will try more.

Thanks.

Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan

________________________________________
差出人: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
送信日時: 2019年11月7日 4:32
宛先: Takeru KAMEDA
CC: NAMD list
件名: Re: namd-l: Multi canonical ensemble method

Hello Takeru, the dependency error is due to trying to measure a total force for a variable type that doesn't have it implemented. Below is the updated link, which unlike the one you copied earlier, should remain the same in future versions (and thus be useful in searches for this message):
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_sys_forcesmedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022498257&sdata=KGEC3nWPOZz%2BwgXQTa21a%2BD5cupKGWNDtC3KPgitk78%3D&reserved=0>

You can still use ABF on an extended-Lagrangian variable, but you probably need to get rid of outputTotalForce. Does that make solve the problem?

The second message about sockets is bogus, sorry. For a while (but not any longer) Colvars has been sharing the error code flag with other functions in NAMD, but it wasn't always set consistently and the numeric code sometimes referred to something completely unrelated, like that. In general, the Colvars module will always print all errors originating there first, and the last "FATAL ERROR" message from the main NAMD function simply refers to that, but does not add any further information.

Giacomo

On Wed, Nov 6, 2019 at 4:58 AM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>> wrote:
Dear Giacomo.

Thank you for your kind reply.

And, I will take care to keep the list in CC.

I changed parentheses to curly braces as :

axis {1, 0, 0} → axis (1, 0, 0)

Then, following error message were output :

Excerpt below

""""""""
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "abf" instance.
colvars: # name = "abf1" [default]
colvars: # colvars = { theta }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # applyBias = on [default]
colvars: # updateBias = on [default]
colvars: # hideJacobian = on
colvars: Jacobian (geometric) forces will be handled internally.
colvars: # fullSamples = 200
colvars: # inputPrefix = [default]
colvars: # outputFreq = 50000 [default]
colvars: # historyFreq = 0 [default]
colvars: # shared = off [default]
colvars: "total force" in colvar theta requires one of the following features, none of which can be enabled:
colvars: -----------------------------------------
colvars: 1. extended Lagrangian
colvars: User-controlled feature "extended Lagrangian" may not be enabled as a dependency in colvar theta.
colvars: 2. total force calculation
colvars: Dynamic feature unavailable: "Jacobian derivative" in cvc tilt0001.
colvars: ...required by "Jacobian derivative" in colvar theta
colvars: ...required by "total force calculation" in colvar theta
colvars: -----------------------------------------
colvars: ...required by "obtain total force" in bias abf1
colvars: Error: Failed dependency in bias abf1.
FATAL ERROR: Error in the collective variables module: Socket operation on non-socket
""""""""

Are there 2 problems ?

In previous exchange for others, I obtained following manual page

http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#x1-530005.3.3oshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022498257&sdata=zJDctIrl0I0IBezXh%2BQ%2F66fPyl65DadfyO%2BIBq5j5pc%3D&reserved=0>

But, I cloudn't resolve above problem

Thanks.

Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan

________________________________________
差出人: Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>>
送信日時: 2019年11月5日 22:18
宛先: Takeru KAMEDA
CC: NAMD list
件名: Re: namd-l: Multi canonical ensemble method

Hello Takeru, please keep the list in CC.

Your error is due to using curly braces instead of parentheses.

Giacomo

On Mon, Nov 4, 2019 at 9:39 PM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>>> wrote:
Dear Giacomo

Thank you for your kind reply.

I tried ABF as you said using attached files.

However, I obtained attached log file (run.log).

Are there any missing configurauin ?

Thanks

Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan

________________________________________
差出人: Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com><mailto:giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>>>
送信日時: 2019年10月30日 23:22
宛先: Takeru KAMEDA
CC: Jérôme Hénin; namd-l
件名: Re: namd-l: Multi canonical ensemble method

Hello Takeru, it looks like you already found the documentation, try to double-check that your configuration is consistent. See here an example:
https://raw.githubusercontent.com/Colvars/colvars/master/tests/spinangle.inp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022508253&sdata=98HCdVmsdAUR3vUK0IOt9ZHlBj7CmXFGJQAPHywsrys%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2FColvars%2Fcolvars%2Fmaster%2Ftests%2Fspinangle.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234920878&sdata=soTnsL1ev1023QcQwGrqktuaU1TLk92cFx00B3PPUwA%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fraw.githubusercontent.com%2FColvars%2Fcolvars%2Fmaster%2Ftests%2Fspinangle.in&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926
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If it is consistent with the doc, do you mind pasting it in the email or attaching it?

Giacomo

On Wed, Oct 30, 2019 at 1:28 AM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp><mailto:kamedapon_at_hiroshima-u.ac.jp<mailto:kamedapon_at_hiroshima-u.ac.jp>>>> wrote:
Hi Jerome.

Thank you for your advice.
And, sorry for the late reply.

I changed the method orientation to spinAngle.
https://www.ks.uiuc.edu/Research/namd/2.13/ug/node55.html#24897a508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022528241&sdata=jXqIBRbJC%2FJnt%2BM6KlD3viB24ltJyhtJBhRDlrOiMh0%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fnamd%2F2.13%2Fug%2Fnode55.html%2324897&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568234930867&sdata=D88d4MWTzKi%2Fw2Atyjk5rNhWkB5%2BqEQxH7kx2M3a2pc%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fnamd%2F2.13%2Fug%2Fnode55.html%2324897&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C6370866
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Now I'm trying such method.
However, I can not set "axis" part in "List of keywords" of spinAngle.

In this case, I think I must set the axis of rotation and center of roration.

Do you know how to set such axis and center.

Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan

________________________________________
差出人: Jérôme Hénin <jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr><mailto:jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr>><mailto:jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr><mailto:jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr>>>>
送信日時: 2019年9月30日 20:49
宛先: Takeru KAMEDA
CC: namd-l
件名: Re: namd-l: Multi canonical ensemble method

Dear Takeru,

this "failed dependency" message indicates that ABF only supports scalar variables. A multidimensional ABF calculation can be done with several scalar variables, not a single vector one.

In this case, the orientation variable is 4-dimensional, which is probably too much for ABF anyway. I recommend reducing your sampling space to 1, 2 or 3 scalar quantities.

Best wishes,
Jerome

Hi. I am trying multi-canonical ensemble method using NAMD2.13.

I wrote colvar file as follows:

colvarsTrajFrequency 5000
colvarsRestartFrequency 50000

colvar {
name theta

    outputValue on
    #outputVelocity on
    #outputEnergy on
    #outputSystemForce on
    #outputAppliedForce on

    orientation {
        atoms { atomnumbers {
                13754 13755 13756 13757 13758 13761 13783 13785 19290 19291 19292 19293 19294 19297 19319 19321
        }}
        refPositionsFile ./colvar.pdb
        refPositionsCol O
    }
}

abf {
   colvars theta
   fullSamples 200
   hideJacobian
}

Then, we execute simulation, following error was output:

Any parts of configulation file was wrong?

Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan

--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
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--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQUMbrWwAdgIUNqb06MEUGcygKgLIHFhp2uZSfG4%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568235000829&sdata=E%2BdGwvkW%2BsPfmPEZ9NqSa%2BU%2BFEljujrZWn9YxDOIA0c%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022668161&sdata=P6%2FxL%2FMbrWwAdgIUNqb06MEUGcygKgLIHFhp2uZSfG4%3D&reserved=0>>
https://github.com/giacomofiorin678157&sdata=E4RR0ysg4ScDg%2BUpTNwKohP81XPR%2BZEQ7KjiDDiRze8%3D&reserved=0><https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgiacomofiorin&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C99bff67013fc40e50bd008d761f2e924%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637085568235010824&sdata=xw%2FHfYOLRpbpy64ed%2F%2FEDVJq6xAgft6I3h2YOnUCrQ8%3D&reserved=0<https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgiacomofiorin&data=02%7C01%7Ckamedapon%40hiroshima-u.ac.jp%7C52f0f5f44b8d47b29ea508d762f0a53e%7Cc40454ddb2634926868d8e12640d3750%7C1%7C0%7C637086658022678157&sdata=E4RR0ysg4ScDg%2BUpTNwKohP81XPR%2BZEQ7KjiDDiRze8%3D&reserved=0>>
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Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQUBaiiTIl7zeHqZE7h9TGUcmVQzFeTyXB4Uug%3D&reserved=0>
https://github.com/giacomofiorin688148&sdata=3h9y1yh%2B2BxxBFiyhT7G4%2BBmwjk3Y%2Bc0hFpTCojkLGI%3D&reserved=0>

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