[gmx-users] probability from COM of micelle

Fri May 10 11:36:38 CEST 2013

Hi,

You indeed could use  the g_rdf command like this (in the script)

g_rdf_mpi -f "$pathXTC" -s "$pathTPR" -n bOG_Micelle_RDF.ndx -norm -com -b $timeBegin1 -e $timeEnd1 -o "$name1"_"$name2"_"$name3"_"$i"_original.xvg < RadDensFunc_"$i".txt

Where in the  RadDensFunc.txt file, i choose as the first group the micelle group (for the micelle COM) and as the second group  the micelle atom you want to plot the rdf (i.e. surfactant headgroup, alkyl tail, etc?)

Do not forget to take into account the (average) volume of the simulation cell and the mass of the atom group to obtain the rho(r) (g.cm-3) as function of the Micelle COM otherwise, you will obtain the N(r) as function of Micelle COM (in nm-1)

HTH

On 5/9/13 10:15 AM, mohammad agha wrote:
>
>
> Dear GROMACS Specialist,
>
> I want to plot probability (nm^-1) distribution of micelle selected atoms with respect to COM of the micelle (nm).
> with respect to this definition, "Probability was defined as the number of instances the selected atom was found within a spherical shell of width 0.02 nm at a distance r from the micelle COM divided by r", may I ask you to give me one formula to plot of this probability, Please?
> for example, to plot of density(nm^-3) with respect to COM of micelle (nm), I do as following:
> density = g(r) * (N/V)
>

It sounds like all you need to do is create a histogram from data produced by
g_dist.  You can make the histogram with g_analyze or any number of other programs.

-Justin

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

------------------------------

Message: 2
Date: Thu, 09 May 2013 21:03:44 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] Fw: probability from COM of micelle
To: gmx-users at gromacs.org
Message-ID: <518BF310.6020303 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 2013-05-09 20:15, Justin Lemkul wrote:
>
>
> On 5/9/13 10:15 AM, mohammad agha wrote:
>>
>>
>> Dear GROMACS Specialist,
>>
>> I want to plot probability (nm^-1) distribution of micelle selected
>> atoms with respect to COM of the micelle (nm).
>> with respect to this definition, "Probability was defined as the
>> number of instances the selected atom was found within a spherical
>> shell of width 0.02 nm at a distance r from the micelle COM divided by
>> r", may I ask you to give me one formula to plot of this probability,
>> Please?
>> for example, to plot of density(nm^-3) with respect to COM of micelle
>> (nm), I do as following:
>> density = g(r) * (N/V)
>>
>
> It sounds like all you need to do is create a histogram from data
> produced by g_dist.  You can make the histogram with g_analyze or any
> number of other programs.
>
> -Justin
>
How about g_rdf?

--
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

------------------------------

Message: 3
Date: Thu, 9 May 2013 13:33:54 -0700
From: Eric Stokes <ess13 at uw.edu>
Subject: [gmx-users] Charmm27 potential energies.
To: gmx-users at gromacs.org
Message-ID:
        <CAPsVVmToRup3GnXTHY6GKOUEvENsTP1QyDhgR7yWeQ-r8VgRjg at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hello,

I am attempting to generate force-field parameters for a fatty acid
molecule that contains a carboxilic acid head group. I decided to use the
parameters for stearic acid as the base for my molecule, since they contain
similar structures with the only major change being a shorter hydrophobic
tail. I noticed that the charge on stearic acid, and other molecules that
have a carboxilic head group, is spread out with -0.9 residing on the head
group and -0.1 on the second carbon. I need to use the protonated from of
my molecule for my simulation, as well as the deprotonated form. I looked
into the parameters for the COOH replacement in the Charmm27 force-field
and used that to form the head group of the protonated form of my molecule.
The problem that I am facing is that this left behind a charge of -0.1 that
resides on the second carbon. Is there any way to find acceptable partial
charges without doing the full Gaussian calculations? I would also
appreciate it if someone could explain why the charges were split onto the
second carbon in the first place.

Thanks in advance,
Eric Stokes

------------------------------

Message: 4
Date: Thu, 09 May 2013 16:39:41 -0400
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Charmm27 potential energies.
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <518C098D.2080100 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 5/9/13 4:33 PM, Eric Stokes wrote:
> Hello,
>
> I am attempting to generate force-field parameters for a fatty acid
> molecule that contains a carboxilic acid head group. I decided to use the
> parameters for stearic acid as the base for my molecule, since they contain
> similar structures with the only major change being a shorter hydrophobic
> tail. I noticed that the charge on stearic acid, and other molecules that
> have a carboxilic head group, is spread out with -0.9 residing on the head
> group and -0.1 on the second carbon. I need to use the protonated from of
> my molecule for my simulation, as well as the deprotonated form. I looked
> into the parameters for the COOH replacement in the Charmm27 force-field
> and used that to form the head group of the protonated form of my molecule.
> The problem that I am facing is that this left behind a charge of -0.1 that
> resides on the second carbon. Is there any way to find acceptable partial
> charges without doing the full Gaussian calculations? I would also
> appreciate it if someone could explain why the charges were split onto the
> second carbon in the first place.
>

Servers exist for this purpose, like SwissParam and ParamChem.  As for the
charge assignments, you would have to investigate the primary literature source
for those parameters and how they were fitted.

-Justin

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

------------------------------

Message: 5
Date: Fri, 10 May 2013 10:05:31 +0530
From: Arunima Shilpi <writetoash28 at gmail.com>
Subject: [gmx-users] groups selection make_ndx -f npt.gro
To: gmx-users at gromacs.org
Message-ID:
        <CAM90emY+dXpYrJdiizJuFVr=F4PTfamcd23dK5vVJaXy7PEOyQ at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hello sir

As in the tutorial for umbrella sampling command

make_ndx -f npt.gro
you have selected two different groups as Chain_A as 19 and Chain_B as 20

If we have protein-ligand interaction whether we should have single group
of protein-ligand complex or we should use two different groups for protein
and ligand.

Regards
Arunima

--

Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer & Epigenetics)
Department of Life Science
National Institute of Technology
Rourkela
Odisha

------------------------------

Message: 6
Date: Thu, 9 May 2013 21:45:10 -0700 (PDT)
From: mohammad agha <mra_bu at yahoo.com>
Subject: [gmx-users] probability from COM of micelle
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID:
        <1368161110.48441.YahooMailNeo at web140902.mail.bf1.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1

Dear GROMACS Specialists,

Thank you very much from your answer, but I want to know plotting this curve from g_rdf.
May I ask you to give me one formula by this command, Please?

Best Regards
Sara

On 2013-05-09 20:15, Justin Lemkul wrote:
>
>
> On 5/9/13 10:15 AM, mohammad agha wrote:
>>
>>
>> Dear GROMACS Specialist,
>>
>> I want to plot probability (nm^-1) distribution of micelle selected
>> atoms with respect to COM of the micelle (nm).
>> with respect to this definition, "Probability was defined as the
>> number of instances the selected atom was found within a spherical
>> shell of width 0.02 nm at a distance r from the micelle COM divided by
>> r", may I ask you to give me one formula to plot of this probability,
>> Please?
>> for example, to plot of density(nm^-3) with respect to COM of micelle
>> (nm), I do as following:
>> density = g(r) * (N/V)
>>
>
> It sounds like all you need to do is create a histogram from data
> produced by g_dist.? You can make the histogram with g_analyze or any
> number of other programs.
>
> -Justin
>
How about g_rdf?

--
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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