Re: [gmx-users] RDF calculation from surface of protein

-surf flag is used with -ref flag. Provide the reference file in the -ref flag. On Thu, Feb 6, 2020 at 1:52 AM Pandya, Akash wrote: > Hi all, > > I am trying to calculate the RDF between the protein surface and the > centre of mass of my ligand and water molecules. Please find below the >

[gmx-users] RDF calculation from surface of protein

Hi all, I am trying to calculate the RDF between the protein surface and the centre of mass of my ligand and water molecules. Please find below the command I used: gmx rdf -s proteinLIG.tpr -f proteinLIG.xtc -n index.ndx -o rdf.xvg -bin 0.02 -cn number.xvg -surf mol -seltype mol_com I get

Re: [gmx-users] RDF between larger molecules

On 1/20/20 10:00 AM, Gmx QA wrote: Thanks Justin! Can you also comment on the other issue, the lack of smoothness? I guess this is because I don't have that many individual coms per bin to accurately compute the rdf? At least I think that makes sense since when I increase the value of -bin in

Re: [gmx-users] RDF between larger molecules

Thanks Justin! Can you also comment on the other issue, the lack of smoothness? I guess this is because I don't have that many individual coms per bin to accurately compute the rdf? At least I think that makes sense since when I increase the value of -bin in gmx rdf I get an increase in

Re: [gmx-users] RDF between larger molecules

On 1/20/20 9:48 AM, Gmx QA wrote: Hi list, I am working on a system that contains lipids, but since there is no water present they do not form a typical bilayer. In these systems I also have some smaller drug-like molecules. What would be the best way to get a proper rdf-function between

[gmx-users] RDF between larger molecules

Hi list, I am working on a system that contains lipids, but since there is no water present they do not form a typical bilayer. In these systems I also have some smaller drug-like molecules. What would be the best way to get a proper rdf-function between the lipids and the drugs? Since both

Re: [gmx-users] rdf

Thank you Justin I will follow On Sun, 10 Nov 2019, 7:05 pm Justin Lemkul, wrote: > > > On 11/9/19 11:17 PM, shakuntala dhurua wrote: > > sir, as i m beginner of gromacs i want to calculate rdf between o-o of > > only bulk water simulation, here i have generate xtc file using gmx rdf > -n > >

Re: [gmx-users] rdf

On 11/9/19 11:17 PM, shakuntala dhurua wrote: sir, as i m beginner of gromacs i want to calculate rdf between o-o of only bulk water simulation, here i have generate xtc file using gmx rdf -n index.ndx -s water5.tpr -f water5.trr -o water5.xtc ,after that for rdf calculation i have used gmx

Re: [gmx-users] rdf

sir, as i m beginner of gromacs i want to calculate rdf between o-o of only bulk water simulation, here i have generate xtc file using gmx rdf -n index.ndx -s water5.tpr -f water5.trr -o water5.xtc ,after that for rdf calculation i have used gmx rdf -n index.ndx -s water5.tpr -f water5.xtc -o

Re: [gmx-users] rdf

On 11/9/19 1:03 AM, shakuntala dhurua wrote: I am facing proble while calculating rdf , after generating xtc file i used flag gmx rdf -s .tpr -f .xtc -n .ndx -o .xvg then from index data i was selected group1 and group2 but there it was written parsed group1 and group2. please suggest me to

[gmx-users] rdf

I am facing proble while calculating rdf , after generating xtc file i used flag gmx rdf -s .tpr -f .xtc -n .ndx -o .xvg then from index data i was selected group1 and group2 but there it was written parsed group1 and group2. please suggest me to solve this problem. -- Gromacs Users mailing list

Re: [gmx-users] RDF in gromacs

What is the selection syntax you are actually using? Copy and paste, don't do from memory. On Wed, 9 Jan. 2019, 8:40 pm daniel madulu shadrack Hi, > I am calculating the rdf of my system as follows. > > 1. rdf of oxygen atom of my drug and water this is successful (I just made > an index file

[gmx-users] RDF in gromacs

Hi, I am calculating the rdf of my system as follows. 1. rdf of oxygen atom of my drug and water this is successful (I just made an index file and for water i choose eg. 5 & a OW) this worked fine. 2. I want now to calculate the rdf of oxygen in my drug and oxygen from the hydroxyl group of the

[gmx-users] RDF in a droplet

Dear all, I have a system contains dispersed molecules of A(# 29) and B(# 14) in water. A droplet is formed by molecule of A and B after 100 ns of MD simulations where the B is supposed to more or less be like a shell around A as a core. I want to know the relative positions of molecules of A and

Re: [gmx-users] rdf coordination number over time (ns)

Hi if you have rdf it is easy to calculate the coordination number by numerical integration https://en.wikibooks.org/wiki/Molecular_Simulation/Radial_Distribution_Functions Arun On Mon, Nov 26, 2018 at 11:38 AM Maria Luisa wrote: > Dear users, > I need to calculate rdf coordination number

[gmx-users] rdf coordination number over time (ns)

Dear users, I need to calculate rdf coordination number over time. I have a pdb trajecory of 200 ns, from which I want to evaluate g(r) and CN of Na-Cl, Na-O, Cl-O. My gromacs works with VMD, but I cannot do coordination number in function of time! Can you help me? Maria Luisa Maria Luisa

Re: [gmx-users] RDF calculations for certain atoms in a polymer

Thank you for your reply! Best regards, Mahsa On Mon, Aug 13, 2018 at 2:47 PM, Mark Abraham wrote: > Hi, > > You need a composite selection, eg of an atomtype and residue type or > molecule type. Make a selection of the atomtype and another of whatever > seems suitable, and combine them. > >

Re: [gmx-users] RDF calculations for certain atoms in a polymer

Hi, You need a composite selection, eg of an atomtype and residue type or molecule type. Make a selection of the atomtype and another of whatever seems suitable, and combine them. Mark On Sat, Aug 11, 2018, 13:53 Mahsa wrote: > Hi Mark, > > Thank you for your reply! > > I tried gmx make_ndx

Re: [gmx-users] RDF calculations for certain atoms in a polymer

Dear Mark, Could you please comment on my previous question? I would really appreciate it. Best regards, Mahsa On Sat, Aug 11, 2018 at 12:52 PM, Mahsa wrote: > Hi Mark, > > Thank you for your reply! > > I tried gmx make_ndx -f topol.tpr -o index.ndx before and then selected > based on the

Re: [gmx-users] RDF calculations for certain atoms in a polymer

Make the selection based on the atomtype and resname Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only

Re: [gmx-users] RDF calculations for certain atoms in a polymer

Hi Mark, Thank you for your reply! I tried gmx make_ndx -f topol.tpr -o index.ndx before and then selected based on the atom types which worked very well. The only problem is I need to also compute the RDF for the O of the side chain with the same atom type as the ester O in the polymer. Then

Re: [gmx-users] RDF calculations for certain atoms in a polymer

Hi, Making a selection with a tool like gmx select or gmx make_ndx is a good way to select e.g. by atomtype. Mark On Sat, Aug 11, 2018, 12:58 Mahsa wrote: > Hello, > > I would like to calculate the RDF between some ions and oxygen atoms of a > polymer. The polymer has ester functional group

[gmx-users] RDF calculations for certain atoms in a polymer

Hello, I would like to calculate the RDF between some ions and oxygen atoms of a polymer. The polymer has ester functional group with two different atom types O and OS according to GAFF. It has also a side chain with ethereal oxygen which has the same atom type as the ester part. How can I

Re: [gmx-users] rdf at contact

I will be grateful if some one can reply my question, Best regards On Wed, May 30, 2018 at 4:45 PM, Faezeh Pousaneh wrote: > Hi, > > I have a system of similar molecules, I would like to obtain the rdf at > contact (meaning, at surface of one particle). > What I try is; I make an index file

Re: [gmx-users] rdf at contact

How noisy is the rdf i.e. what is the bin width, how many atoms etc? Have you graphed the entire function? That would be my first suggestion of the cause. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal

[gmx-users] rdf at contact

Hi, I have a system of similar molecules, I would like to obtain the rdf at contact (meaning, at surface of one particle). What I try is; I make an index file containing only central atoms of all molecules, then I run: gmx rdf -f NPT.xtc -s NPT.tpr -n index.ndx -pbc -ref 1 -sel 0 -b

[gmx-users] RDF

Dear all, I wan to parameterize the interaction between coarse-grained beads of a molecule and beads of P$ martini water using Votca. So, I want to calculate the RDF between moecules's beads and water beads in atomistic level as target RDF. I know the mapping of the molecule itself so that I know

[gmx-users] RDF calculation

Dear all, I have a curved rod-like micelle formed by three different molecules. I want to calculate the RDF of constituent molecules. I want to select the center line of the curved cylindir-like structure as a reference point. How can I do that? I am using Gromacs version 5.1.2. with Martini

Re: [gmx-users] RDF brads

You can just give the selection you would use to make the ndx file directly to gmx rdf. You should be fine to average the simulations RDF (and e.g. PCA) are statistical properties, and averaging should give you better statistics =) On Wed, Mar 28, 2018 at 11:56 PM, Alex

[gmx-users] RDF brads

Dear all, To obtain the coarse-graine (CG) parameters of a molecule using votca, below are the considered beads: (the bead are weighted by atomic weights ) Bead A contains atoms of " a1, ..., a11" Bead B contains atoms of " b1, ..., b9" Bead C contains atoms of " c1,..., c13" Now, to calculate

Re: [gmx-users] rdf calculation for wormlike micelles

Dear Joe, Sorry for the confusion. I am working with martini force field and I have three different molecules in the micelle structure. I want to analyze the RDF of the constituent molecules with respect to the line that pass through the center along with its length. As I mention before this line

Re: [gmx-users] rdf calculation for wormlike micelles

You cannot use a line as the reference. From a brief glance at the paper you link it seems like maybe you actually want to compute the expectation value of the micelle backbone, a method known as principle curves which is a generalization of principle component analysis. At any rate, you should

Re: [gmx-users] rdf calculation for wormlike micelles

Dear Joe, Sorry for the confusion. I am working with martini force field and I have three different molecules in the micelle structure. I want to analyze the RDF of the constituent molecules with respect to the line that pass through the center along with its length. As I mention before this line

Re: [gmx-users] rdf calculation for wormlike micelles

See here for info on the selection syntax http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html On Wed, Mar 14, 2018 at 10:01 AM, Esra Kaçar wrote: > Dear all, > > I am working on a wormlike micelle that has a curved structure. I want to > calculate the

[gmx-users] rdf calculation for wormlike micelles

Dear all, I am working on a wormlike micelle that has a curved structure. I want to calculate the radial distribution functions of constituent molecules with respect to the backbone (the line following the micelle length and represents the center of the curved cylindrical structure) of the

Re: [gmx-users] RDF from NPT simulation?

On 11/2/17 7:28 AM, Sudip Das wrote: Dear Justin, Should I have to use any flag(s) with 'rdf' module to scale the coordinates for fixing the box size? I didn't find such flag in 'rdf' module. There are no special flags. GROMACS commands deal with box vectors intrinsically. -Justin --

Re: [gmx-users] RDF from NPT simulation?

Dear Justin, Should I have to use any flag(s) with 'rdf' module to scale the coordinates for fixing the box size? I didn't find such flag in 'rdf' module. Please help. Regards, Sudip On Thu, Nov 2, 2017 at 4:41 PM, Justin Lemkul wrote: > > > On 11/2/17 6:39 AM, Sudip Das

Re: [gmx-users] RDF from NPT simulation?

On 11/2/17 6:39 AM, Sudip Das wrote: Dear All, Is it possible to calculate RDF from GROMACS module 'rdf' from a NPT simulation trajectory (where box size changes from frame to frame)? Yes. -Justin -- == Justin A. Lemkul, Ph.D. Assistant

[gmx-users] RDF from NPT simulation?

Dear All, Is it possible to calculate RDF from GROMACS module 'rdf' from a NPT simulation trajectory (where box size changes from frame to frame)? Thanks in advance. Regards, Sudip -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] RDF

No idea what a surface distribution function is, and how it is generated. But I suspect that those two are not the same. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052

Re: [gmx-users] RDF

Thank you Sir, Is spatial distribution function is same as that of surface distribution function? On Wed, Aug 23, 2017 at 9:39 AM, Dallas Warren wrote: > https://www.google.com.au/search?q=gromacs+sdf > > i.e. gmx spatial > > Unfortunately, it only currently will work

Re: [gmx-users] RDF

https://www.google.com.au/search?q=gromacs+sdf i.e. gmx spatial Unfortunately, it only currently will work for a single reference molecule. There use to be a g_sdf that would work for multiple copies of the reference, much in the same manner that gmx rdf does. So if that is what you are after,

Re: [gmx-users] RDF

Dear Warren, Thanks a lot. How will I be able to calculate SDF using Gromacs..? On Wed, 23 Aug 2017 at 8:19 AM, Dallas Warren wrote: > SDF (Spatial Distribution Function) is simply a three dimensional RDF. > So instead of simply having a probability associated with

Re: [gmx-users] RDF

SDF (Spatial Distribution Function) is simply a three dimensional RDF. So instead of simply having a probability associated with each radius (r), it provides a probability associated with each (x,y,z) point. VMD can display the SDF generated by GROMACS. Catch ya, Dr. Dallas Warren Drug Delivery,

Re: [gmx-users] RDF

> > I have come across people describing RDF analysis between water and water > and I always wonder what does it means. RDF can be done between protein and > water to know the distribution of water around protein with default center > of mass(My little knowledge) and what co-ordination number

Re: [gmx-users] RDF

Hi Dan Thank you so much for you descriptive answers. I have few clarifications that I have posted here. I will go through the papers here. On Fri, Aug 18, 2017 at 5:01 PM, Dan Gil wrote: > Hi Rahul, > > I can't find the exact papers right now, but I remember seeing some

Re: [gmx-users] RDF

Hi Rahul, I can't find the exact papers right now, but I remember seeing some inconsistency in how people name these functions especially the radial distribution function and pair correlation functions. If we go far back into literature, we can see JG Kirkwood using pair correlation functions as

Re: [gmx-users] RDF Values

I think you can use -cut 0 -rmax 1.5 this will give you the RDF upto 1.5 nm.- Message from "Pandya, Akash" <akash.pandya...@ucl.ac.uk> -     Date: Mon, 31 Jul 2017 07:29:19 +     From: "Pandya, Akash" <akash.pandya...@ucl.ac.uk> Reply-To: gmx-us...

Re: [gmx-users] RDF Values

hi dear!can anyone please suggest me what does it mean."In chosen Force field there is no residue type for QLN"there was no QLN in our origin file. There is always a problem when i select any force field.regards On Monday, 31 July 2017, 12:29, "Pandya, Akash"

[gmx-users] RDF Values

Hi all, I am calculating the RDF from a particular residue to a particular glycine molecule. I created an index file for both to do this. My simulation box is 1.5nm, but the RDF values are in the range of 2nm-3nm. I have viewed my trajectory and all the components stay inside the box. Please

Re: [gmx-users] RDF

Dear Vidya.R Its very difficult to answer this question.It depends on your system .If you run more time of your system, RDF will be more smooth Saikat Pal IIT GUWAHATI On Wednesday 12 July 2017, 10:02:30 AM IST, Vidya R wrote: Hi, I want to calculate RDF of my

[gmx-users] RDF

Hi, I want to calculate RDF of my organic molecule with a solvent. What should be the duration of my simulation? Is 100 ps enough? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] RDF

On 7/11/17 1:38 PM, Pandya, Akash wrote: When I try to make an index group for the protein residue and the ligand molecule, the whole system is included in the index file. I use these options: r 166 (protein residue) r 901 (ligand molecule) then press q All the default groups will

Re: [gmx-users] RDF

...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: 11 July 2017 18:06 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] RDF On 7/11/17 11:41 AM, Pandya, Akash wrote: > Hi, > > I want to calculate the RDF between a specifi

Re: [gmx-users] RDF

On 7/11/17 11:41 AM, Pandya, Akash wrote: Hi, I want to calculate the RDF between a specific residue and a ligand molecule in my simulation box. Is this possible and do I have to make a special index group for that? If so how would I go about doing that? By using make_ndx or a suitable

[gmx-users] RDF

Hi, I want to calculate the RDF between a specific residue and a ligand molecule in my simulation box. Is this possible and do I have to make a special index group for that? If so how would I go about doing that? Thanks, Akash -- Gromacs Users mailing list * Please search the archive at

[gmx-users] RDF OF PROTEIN - LIGAND

Hi, After simulations, can we plot the rdf of protein and ligand interaction? How to refine the analysis? Can anyone suggest suitable books / papers to interpret protein ligand radial distribution funtion? Thanks, Neha -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] RDF of a group around CNT axis

I noticed that the gmx rdf some how cannot find the center of mass (COM) for the CNT because after that I manually put a single particle in the COM of the CNT and calculated the rdf around it (with -xy option), the gmx rdf resulted the expected value which is a sharp peak at the radius of the cnt.

Re: [gmx-users] RDF of a group around CNT axis

Dear Srinivas, That's absolutely right, I want to calculate the RDF of a certain group around the central axis of a nanotube. And as I know that the RDF of the CNT around its axis is just a sharp peak at the radius, I just tested the command-line parameters for this case, to specify that which

Re: [gmx-users] RDF of a group around CNT axis

If I understand you correctly: you want to calculate the RDF of a certain group (NOT part of the nanotube) around the central axis of a nanotube? The way I do these calculations is to use the gmx trjconv tool to isolate a trajectory file of ONLY the gropus I am interested in and run my

[gmx-users] RDF of a group around CNT axis

Dear experts, I want to calculate rdf of a certain group around the axis of a cnt, but I do not know what are the proper parameters to choose in the command-line. To test the parameters, I calculated the rdf of cnt itself around its axis which must be a sharp peak at the cnt radius. I tested the

[gmx-users] RDF calculation

Dear gmx-users, I am new to Gromacs. I have a droplet including some types of lipids such as DPPC. I want to calculate RDF for head atom of DPPC with respect to droplet center-of-mass. My question is how can i calculate this issue in versions 2017. Apparently this feature has been removed from

[gmx-users] rdf calculation with respect to center of mass

Dear gmx-users, The radial distribution function with respect to center-of-mass was computable in old gromacs versions. How can I calculate that  in newer version(2016)? Thanks in advance. Maryam -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] RDF convergence

Mine converges. What about box size? On Fri, Dec 4, 2015 at 7:14 AM, Sudip Das wrote: > Hi, > > I am using g_rdf command (within gromacs-5.0.5) to calculate rdf as follow: > > g_rdf_mpi_d -f .xtc -n .ndx -o rdf -cn > > But the rdf is not getting converged to 1

[gmx-users] RDF convergence

Hi, I am using g_rdf command (within gromacs-5.0.5) to calculate rdf as follow: g_rdf_mpi_d -f .xtc -n .ndx -o rdf -cn But the rdf is not getting converged to 1 exactly, rather it converges to approximately 1.03. Whenever I am calculating rdf like this for different sets of atoms, I am getting

[gmx-users] RDF com

Hello, I am trying to calculate the rdf using the center of mass of a sulfonate group, SO3 with other SO3 groups in the system. The SO3 group is part of a bigger molecule. Is it appropriate to use gmx rdf -rdf mol_com to carry out this operation or should I use the gmx rdf -yescom In each

Re: [gmx-users] RDF com

Thanks a lot, Justin. On Sat, Oct 17, 2015 at 8:02 AM, Justin Lemkul wrote: > > > On 10/17/15 5:32 AM, Deva Priya wrote: > >> Hello, >> >> I am trying to calculate the rdf using the center of mass of a sulfonate >> group, SO3 with other SO3 groups in the system. The SO3 group

Re: [gmx-users] RDF com

On 10/17/15 5:32 AM, Deva Priya wrote: Hello, I am trying to calculate the rdf using the center of mass of a sulfonate group, SO3 with other SO3 groups in the system. The SO3 group is part of a bigger molecule. Is it appropriate to use gmx rdf -rdf mol_com to carry out this operation or

Re: [gmx-users] RDF

Search for my papers Vitaly V. Chaban. You will find many papers determining solvation/solubility, where it is described how solubility can be obtained from atomistic simulations. RDF alone is not a proper descriptor. However, if you plot COM-COM RDF for C60, you will get some solubility related

[gmx-users] RDF

Dear all, I have attempted to show the dynamics of a C60 molecule in presence of aqueous soluble binders. I am using GROMOS53A6 force field and SPC/E water. I took the pdb as well as the itp file of both from the ATB server. I ran simulations using GROMACS 4.5.6 of fullerene both in

Re: [gmx-users] RDF

you cannot predict solubility using the radial distribution of solvent molecules around a single solute, single molecules just cannot aggregate into a separate phase, so your system is too simple to provide the information you want. even if you succeed in the thermodynamic integration, it will

[gmx-users] RDF for molecules above a surface

Dear all, I would like to find out the distribution of molecules above a flat surface, such as the surface of a membrane. Would it be appropriate to be using: gmx rdf -f run.xtc -s run.tpr -n index.ndx -surf mol -rdf mol_com -pbc After staring at the manual for really long, I can't quite figure

Re: [gmx-users] RDF

Thanks Justin! I cant find so much details in the manual; there are only general facts. does g_density give partial density? On Mon, May 18, 2015 at 11:25 AM, mah maz mahma...@gmail.com wrote: Hi Justin The fact is I want to calculate water density in the system. If I select group1: oxygen

Re: [gmx-users] RDF

On 5/19/15 4:12 AM, mah maz wrote: Thanks Justin! I cant find so much details in the manual; there are only general facts. does g_density give partial density? Read the first sentence of the help description :) -Justin On Mon, May 18, 2015 at 11:25 AM, mah maz mahma...@gmail.com wrote:

Re: [gmx-users] RDF

Hi Justin The fact is I want to calculate water density in the system. If I select group1: oxygen and group2: oxygen, g_rdf command gives me very large numbers. Is it the number of atoms that should be changed to g/cm3? Besides, what does it calculate, each O is a reference atom during

Re: [gmx-users] RDF

On 5/18/15 2:55 AM, mah maz wrote: Hi Justin The fact is I want to calculate water density in the system. If I select group1: oxygen and group2: oxygen, g_rdf command gives me very large numbers. Is it the number of atoms that should be changed to g/cm3? Besides, what does it calculate, each O

[gmx-users] RDF

Dear all, I want to calculate the radial distribution function of water molecules in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which is not logical I suppose. Is it meaningful if I separate oxygen and hydrogen atoms in the index file and calculate the RDF for O-O atoms?

Re: [gmx-users] RDF

On 5/17/15 5:47 AM, mah maz wrote: Dear all, I want to calculate the radial distribution function of water molecules in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which is not logical I suppose. Is it meaningful if I separate oxygen and hydrogen atoms in the index file

Re: [gmx-users] RDF plot with large g(r) values

:34 AM, Kester Wong kester2...@ibs.re.kr wrote: Hi Andre, Thank you for your input. *보낸사람* : André Farias de Moura mo...@ufscar.br *받는사람* : Discussion list for GROMACS us gmx-us...@gromacs.org *받은날짜* : 2015년 1월 8일(목) 22:05:39 *제목* : Re: [gmx-users] RDF plot with large g(r) values RDF

Re: [gmx-users] RDF plot with large g(r) values

Hi Andre,Thank you for your input.보낸사람 : "André Farias de Moura" mo...@ufscar.br받는사람 : Discussion list for GROMACS us gmx-us...@gromacs.org받은날짜 : 2015년 1월 8일(목) 22:05:39제목 : Re: [gmx-users] RDF plot with large g(r) valuesRDF values are sensitive to the volume of the system, so if you put

Re: [gmx-users] RDF plot with large g(r) values

Dear Justin, No, I am not comparing equivalent systems, nor reproducing previous findings. My simulation box contains a droplet of 2000 water molecules on graphene.The RDF of g(r) Ow-Ow shows a first peak at r = 0.3 nm, with a peak height of 400.For 6000 and 10,000 water molecules, the peak

Re: [gmx-users] RDF plot with large g(r) values

On 1/8/15 4:48 AM, Kester Wong wrote: Dear all, My apologies if this question sounds too basic of if it has been covered. I did some RDF calculations, and as when I plotted the figures, the g(r) values are in the hundreds, whereas the papers that I have seen are all in the range of 0-12.

Re: [gmx-users] RDF plot with large g(r) values

RDF values are sensitive to the volume of the system, so if you put the same solutes inside a larger/smaller box, RDF values change accordingly (check basic definitions of RDF in simulation handbooks to make sure you understand this relation). and even if you have the same size and composition,

[gmx-users] RDF does not reach 1 for bulk

Dear Gromacs users, I would like to know why the normalized RDF data from g_rdf does not reach 1 for bulk? As an alternative I tried using the raw data (i.e., by using the 'nonorm' flag) and normalized the values by dividing them by 'rho*volume of bin', which I believe is the standard method

[gmx-users] RDF calculation.

Hi, I am studying the dynamics of a double stranded DNA in presence of small molecules. I want to study the preferential binding of these molecules in the grooves and backbones of the DNA and also calculate the feasibility of these binding in terms of calculating the free energy change.My

Re: [gmx-users] RDF calculation.

Well, since you are not interested in the duplex stability, I would not use -COM. See, during the simulation, the center-of-mass of such a small helix part can drastically move, leading to a questionable result. Check your system and make sure that you will not face this situation. About the PMF,

Re: [gmx-users] RDF calculation.

On 12/27/14 4:17 AM, soumadwip ghosh wrote: Hi, I am studying the dynamics of a double stranded DNA in presence of small molecules. I want to study the preferential binding of these molecules in the grooves and backbones of the DNA and also calculate the feasibility of these binding in

Re: [gmx-users] RDF analysis with respect to center of mass of rotein

On 9/18/14 4:45 PM, Carlos Navarro Retamal wrote: Hi Justin, First of all thanks for your reply. It worked, but i’m getting weird results. When i measured the RDF between: Protein (COM) - Glycerol (the entire molecule) i got a huge pick at 0.022 nm, which doesn’t make any sense (because i

Re: [gmx-users] RDF analysis with respect to center of mass of otein

I Justin, Thanks for your reply. Sadly, that’s not the only bizarre peak,as you can see on the next image: http://cl.ly/1B3B2y3I0o1R This is how it looks when i don’t consideren the COM as a reference: http://cl.ly/3m0d2W2y0N1Y What; i your opinion, could be the problem? I think i’ll just have to

Re: [gmx-users] RDF analysis with respect to center of mass of otein

On 9/19/14 4:54 PM, Carlos Navarro Retamal wrote: I Justin, Thanks for your reply. Sadly, that’s not the only bizarre peak,as you can see on the next image: http://cl.ly/1B3B2y3I0o1R This is how it looks when i don’t consideren the COM as a reference: http://cl.ly/3m0d2W2y0N1Y What; i your

Re: [gmx-users] RDF analysis with respect to center of mass of otein

Not at all. I’m using the .xtc file that comes from the simulation. What do you mean with the nrexcl issue? Is there a way i can fix it? -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations

Re: [gmx-users] RDF analysis with respect to center of mass of otein

Hi Justin, Thanks again for all your help. If the problem is related to periodicity, why if i consider the whole protein i got ‘normal’ results? In any case i centered the protein with the following command: trjconv -f npt_production.xtc -s npt_production.tpr -center -pbc mol -o

Re: [gmx-users] RDF analysis with respect to center of mass of otein

On 9/19/14 6:07 PM, Carlos Navarro Retamal wrote: Hi Justin, Thanks again for all your help. If the problem is related to periodicity, why if i consider the whole protein i got ‘normal’ results? A normal (non-COM-based) RDF is an atom-based RDF, so periodicity doesn't affect the outcome.

Re: [gmx-users] RDF analysis with respect to center of mass of otein

Carlos, You might want to try a PBC correction with -pbc nojump and another RDF calculation with the corrected trajectory. 2014-09-19 19:10 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 9/19/14 6:07 PM, Carlos Navarro Retamal wrote: Hi Justin, Thanks again for all your help. If the problem

Re: [gmx-users] RDF analysis with respect to center of mass of otein

Hi Marcelo, Thanks for your reply. Sadly it didn’t work either, so i’m trying to generate a new .tpr file by changing the nrexcl values just as Justin suggest. Hope this may works. Thanks the two of you. Best Regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied

[gmx-users] RDF analysis with respect to center of mass of Protein

Dear gromacs users, In order to measure the interactions between a Protein with respect to a mixture solvent solution (glycerol-water) i’m trying to measure the RDF between the protein with respect to the C and O atoms of Glycerol respectively. By now i have measured g(r) between: Protein -

Re: [gmx-users] RDF analysis with respect to center of mass of Protein

On 9/18/14 2:04 PM, Carlos Navarro Retamal wrote: Dear gromacs users, In order to measure the interactions between a Protein with respect to a mixture solvent solution (glycerol-water) i’m trying to measure the RDF between the protein with respect to the C and O atoms of Glycerol

Re: [gmx-users] RDF analysis with respect to center of mass of rotein

Hi Justin, First of all thanks for your reply. It worked, but i’m getting weird results. When i measured the RDF between: Protein (COM) - Glycerol (the entire molecule) i got a huge pick at 0.022 nm, which doesn’t make any sense (because i presumed that at this distance there must be a steric

Re: [gmx-users] RDF of solvation shell molecules

On 5/23/14, 12:37 AM, sujithkakkat . wrote: Hello Chandan, Thank you for the response. I have used g_rdf, but I guess it gives the RDF for the whole system. Say, if I choose water oxygen, it will plot RDF from water molecules in the whole system. But, I want the RDF for the solvation

[gmx-users] RDF of solvation shell molecules

Hello, I would like to know if it is possible to plot the RDF of water molecules belonging to the solvation shell of a solute. I mean, I want to know the effect of the solute on the water arrangement in the solvation shell. Is there a way to do this? Regards, Sujith. -- Gromacs Users

  1   2   >