[gmx-users] Tilt angle
asasa qsqs
sanaz_dr_m at yahoo.com
Thu Mar 12 23:46:21 CET 2015
Dear Justin,I want to calculate the tilt angle of DPPC, which command must be used?Thank you,Mrs.Mahdavi
On Thursday, March 12, 2015 10:49 PM, "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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Today's Topics:
1. Re: umbrella sampling tutorial (Justin Lemkul)
2. Re: trajectory film (Justin Lemkul)
3. boron atom (Faezeh Pousaneh)
4. boron atom (Faezeh Pousaneh)
5. Re: Dihedral angle autocorrelation function - g_chi function
mismatch (atanu das)
6. Re: Dihedral angle autocorrelation function - g_chi function
mismatch (atanu das)
7. Re: Dihedral angle autocorrelation function - g_chi function
mismatch (David van der Spoel)
----------------------------------------------------------------------
Message: 1
Date: Thu, 12 Mar 2015 07:50:17 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] umbrella sampling tutorial
Message-ID: <55017D79.40308 at vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 3/12/15 2:41 AM, Ming Tang wrote:
>
> Dear Justin,
>
> The results turned out that the COM distance between them is the same over time, seems that both Chain_A and Chain_B had been pulled by the same force in the same direction, which is different from the tutorial.
>
Switch Chain_A and Chain_B in the .mdp file.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 2
Date: Thu, 12 Mar 2015 07:51:20 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] trajectory film
Message-ID: <55017DB8.5080804 at vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 3/12/15 2:23 AM, mah maz wrote:
> Dear all,
> I have a question probably not related to this mailing list! I want to see
> a film of an output trajectory via VMD. I tried the .trr file by the
> appropriate format in VMD, it shows that the frames are being constructed
> and rendering is complete but nothing can be seen. Is there a problem with
> my .trr file? Can anyone help me in this regard?
There is a VMD mailing list that is more appropriate for this question.
Make sure you load the initial coordinates first, then load the .trr as data for
those coordinates. You can't just load a .trr (or any trajectory) by itself.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 3
Date: Thu, 12 Mar 2015 14:16:50 +0100
From: Faezeh Pousaneh <fpoosaneh at gmail.com>
To: gmx-users <gmx-users at gromacs.org>,
gromacs.org_gmx-users-request at maillist.sys.kth.se,
gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] boron atom
Message-ID:
<CAJtnTaUA+xGZyx7hzc31T1dR2ucJBXGgDmryJLFFKARarRFkWQ at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
Does any one know which force filed contains 'Boron' atom? I need it for
my simulation, molecule sodium tetraphenylborate.
Best regards
------------------------------
Message: 4
Date: Thu, 12 Mar 2015 14:16:50 +0100
From: Faezeh Pousaneh <fpoosaneh at gmail.com>
To: gmx-users <gmx-users at gromacs.org>,
gromacs.org_gmx-users-request at maillist.sys.kth.se,
gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] boron atom
Message-ID:
<CAJtnTaUA+xGZyx7hzc31T1dR2ucJBXGgDmryJLFFKARarRFkWQ at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
Does any one know which force filed contains 'Boron' atom? I need it for
my simulation, molecule sodium tetraphenylborate.
Best regards
------------------------------
Message: 5
Date: Thu, 12 Mar 2015 18:03:51 +0000 (UTC)
From: atanu das <samrucu at yahoo.co.in>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>,
"gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>, atanu das
<samrucu at yahoo.co.in>
Subject: Re: [gmx-users] Dihedral angle autocorrelation function -
g_chi function mismatch
Message-ID:
<464696977.1016825.1426183431684.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8
Hi again,
Just to add a note ---
It seems that g_angle can also calculate the dihedral angle autocorrelation function with the option -oc. Does this program use the same functional form as g_chi i.e. is the functions defined as ---
C(t) = <cos(theta(tau))?cos(theta(tau+t)) >
ThanksAtanu?
On Wednesday, 11 March 2015 9:13 PM, atanu das <samrucu at yahoo.co.in> wrote:
Hi All,
As Prof. David van der Spoel referred in the last communication about how the dihedral angle autocorrelation function is calculated via the program g_chi, I have a query regarding the differences that I found between the function mentioned in the article (Biophys. J. 72 pp. 2032-2041 (1997)) and the function used by the program g_chi.
According to the article, the dihedral angle autocorrelation function is defined as:
C(t) = <cos[theta(tau)-theta(tau+t)]> ..... (Eq. 1 of the article)
However, the g_chi program uses the function:
C(t) = <cos(theta(tau))?cos(theta(tau+t)) > ..... (Eq. 2)
So, apparently the g_chi program uses a different function. Am I correct? Is there a way around it? I mean is there a way to estimate C(t) using the function given in the article (Eq. 1)?
ThanksAtanu?
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------------------------------
Message: 6
Date: Thu, 12 Mar 2015 18:03:51 +0000 (UTC)
From: atanu das <samrucu at yahoo.co.in>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>,
"gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>, atanu das
<samrucu at yahoo.co.in>
Subject: Re: [gmx-users] Dihedral angle autocorrelation function -
g_chi function mismatch
Message-ID:
<464696977.1016825.1426183431684.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8
Hi again,
Just to add a note ---
It seems that g_angle can also calculate the dihedral angle autocorrelation function with the option -oc. Does this program use the same functional form as g_chi i.e. is the functions defined as ---
C(t) = <cos(theta(tau))?cos(theta(tau+t)) >
ThanksAtanu?
On Wednesday, 11 March 2015 9:13 PM, atanu das <samrucu at yahoo.co.in> wrote:
Hi All,
As Prof. David van der Spoel referred in the last communication about how the dihedral angle autocorrelation function is calculated via the program g_chi, I have a query regarding the differences that I found between the function mentioned in the article (Biophys. J. 72 pp. 2032-2041 (1997)) and the function used by the program g_chi.
According to the article, the dihedral angle autocorrelation function is defined as:
C(t) = <cos[theta(tau)-theta(tau+t)]> ..... (Eq. 1 of the article)
However, the g_chi program uses the function:
C(t) = <cos(theta(tau))?cos(theta(tau+t)) > ..... (Eq. 2)
So, apparently the g_chi program uses a different function. Am I correct? Is there a way around it? I mean is there a way to estimate C(t) using the function given in the article (Eq. 1)?
ThanksAtanu?
--
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------------------------------
Message: 7
Date: Thu, 12 Mar 2015 20:18:47 +0100
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Dihedral angle autocorrelation function -
g_chi function mismatch
Message-ID: <5501E697.1060701 at xray.bmc.uu.se>
Content-Type: text/plain; charset=utf-8; format=flowed
On 2015-03-12 19:03, atanu das wrote:
> Hi again,
> Just to add a note ---
> It seems that g_angle can also calculate the dihedral angle autocorrelation function with the option -oc. Does this program use the same functional form as g_chi i.e. is the functions defined as ---
> C(t) = <cos(theta(tau)) cos(theta(tau+t)) >
I don't think so, but please check the source code if unsure.
> ThanksAtanu
>
> On Wednesday, 11 March 2015 9:13 PM, atanu das <samrucu at yahoo.co.in> wrote:
>
>
> Hi All,
> As Prof. David van der Spoel referred in the last communication about how the dihedral angle autocorrelation function is calculated via the program g_chi, I have a query regarding the differences that I found between the function mentioned in the article (Biophys. J. 72 pp. 2032-2041 (1997)) and the function used by the program g_chi.
> According to the article, the dihedral angle autocorrelation function is defined as:
> C(t) = <cos[theta(tau)-theta(tau+t)]> ..... (Eq. 1 of the article)
>
> However, the g_chi program uses the function:
> C(t) = <cos(theta(tau)) cos(theta(tau+t)) > ..... (Eq. 2)
> So, apparently the g_chi program uses a different function. Am I correct? Is there a way around it? I mean is there a way to estimate C(t) using the function given in the article (Eq. 1)?
> ThanksAtanu
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
------------------------------
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