Hi,
Thank you very much from your answer, but I think this is about numerical density (g(r)*(N/V)) or mass density (g(r)*(m/V))? I want to know about probability(nm^-1) with g_rdf, Please? Best Regards Sara ----- Forwarded Message ----- From: ABEL Stephane 175950 <[email protected]> To: "[email protected]" <[email protected]> Cc: Sent: Friday, May 10, 2013 2:06 PM Subject: [gmx-users] probability from COM of micelle 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 <[email protected]> Subject: Re: [gmx-users] Fw: probability from COM of micelle To: [email protected] Message-ID: <[email protected]> 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. [email protected] http://folding.bmc.uu.se ------------------------------ Message: 3 Date: Thu, 9 May 2013 13:33:54 -0700 From: Eric Stokes <[email protected]> Subject: [gmx-users] Charmm27 potential energies. To: [email protected] Message-ID: <capsvvmtorup3gnxthy6gkouevenstp1qydhgr7yweq-r8vg...@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 <[email protected]> Subject: Re: [gmx-users] Charmm27 potential energies. To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> 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 <[email protected]> Subject: [gmx-users] groups selection make_ndx -f npt.gro To: [email protected] Message-ID: <CAM90emY+dXpYrJdiizJuFVr=f4ptfamcd23dk5vvjaxy7pe...@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 <[email protected]> Subject: [gmx-users] probability from COM of micelle To: "[email protected]" <[email protected]> Message-ID: <[email protected]> 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. [email protected]? ? http://folding.bmc.uu.se -- gmx-users mailing list? ? [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? 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