[gmx-users] RMSD of a single water molecule.

Dear User, I am trying to find the RMSD of a single water molecule which showed H-bond interaction with a ligand in a protein-ligand system simulation. The study was to explore the role of water in the binding of the ligand at the receptor. The RMSD of the water molecule (using the protein

Re: [gmx-users] RMSD analysis of protein-ligand complex

Thank you Your advice is very helpful I will try to reparametrize the molecule, which I think is a better strategy. On Sun, Oct 6, 2019 at 6:38 AM Justin Lemkul wrote: > > > On 10/5/19 1:58 PM, Quin K wrote: > > Thank you. > > > > I examined the trajectory using VMD and noted that ligand had

Re: [gmx-users] RMSD analysis of protein-ligand complex

On 10/5/19 1:58 PM, Quin K wrote: Thank you. I examined the trajectory using VMD and noted that ligand had come out of the binding site and is running around. How is this possible? I have used the guidelines in mdtutorials.com to set up the system. However it's worth noting that there was a

Re: [gmx-users] RMSD analysis of protein-ligand complex

Thank you. I examined the trajectory using VMD and noted that ligand had come out of the binding site and is running around. How is this possible? I have used the guidelines in mdtutorials.com to set up the system. However it's worth noting that there was a power failure around the same time

Re: [gmx-users] RMSD analysis of protein-ligand complex

On 10/5/19 11:59 AM, Quin K wrote: Thank you. I got following when I analysed Ligand RMSD protein backbone as east square fit. Graph Can you please comment why there's high fluctuation after like 23 ns? What could this mean? Watch the

Re: [gmx-users] RMSD analysis of protein-ligand complex

Thank you. I got following when I analysed Ligand RMSD protein backbone as east square fit. Graph Can you please comment why there's high fluctuation after like 23 ns? What could this mean? Thanks Regards! On Sat, Oct 5, 2019 at 9:08 PM Justin

Re: [gmx-users] RMSD analysis of protein-ligand complex

On 10/5/19 11:36 AM, Quin K wrote: OK thanks. What should I pick for least square fit in following instances for example. *RMSD of* 1. protein backbone+ligand 2. protein backbone 3. lingad only I've already answered that. And again, it always depends on the question you are asking. You

Re: [gmx-users] RMSD analysis of protein-ligand complex

OK thanks. What should I pick for least square fit in following instances for example. *RMSD of* 1. protein backbone+ligand 2. protein backbone 3. lingad only On Sat, Oct 5, 2019 at 8:56 PM Justin Lemkul wrote: > > > On 10/5/19 11:24 AM, Quin K wrote: > > Thank you! > > How important is the

Re: [gmx-users] RMSD analysis of protein-ligand complex

On 10/5/19 11:24 AM, Quin K wrote: Thank you! How important is the least square fit in these RMSD calculations? Very; it determines how to interpret the result. Or should I just pick system for least square fit all time? You should never pick "System" for a fit. -Justin On Sat, Oct

Re: [gmx-users] RMSD analysis of protein-ligand complex

Thank you! How important is the least square fit in these RMSD calculations? Or should I just pick system for least square fit all time? On Sat, Oct 5, 2019 at 8:45 PM Justin Lemkul wrote: > > > On 10/5/19 11:11 AM, Quin K wrote: > > To see if complex is stable and to see how it fluctuate in

Re: [gmx-users] RMSD analysis of protein-ligand complex

On 10/5/19 11:11 AM, Quin K wrote: To see if complex is stable and to see how it fluctuate in the binding site. Stability of the complex can mean multiple things. If you want to show that the protein structure is stable in the presence of the ligand, you would compute the RMSD of the

Re: [gmx-users] RMSD analysis of protein-ligand complex

To see if complex is stable and to see how it fluctuate in the binding site. On Sat, Oct 5, 2019 at 8:33 PM Justin Lemkul wrote: > > > On 10/5/19 10:53 AM, Quin K wrote: > > Hi, > > > > *What should I pick for RMSD analysis of protein ligand complex? * > > *What other analysis can be done for

Re: [gmx-users] RMSD analysis of protein-ligand complex

On 10/5/19 10:53 AM, Quin K wrote: Hi, *What should I pick for RMSD analysis of protein ligand complex? * *What other analysis can be done for protein ligand complex? * Following are the options I have for least square fit and for RMSD calculation. MPPA is the ligand I used. Group 0 (

[gmx-users] RMSD analysis of protein-ligand complex

Hi, *What should I pick for RMSD analysis of protein ligand complex? * *What other analysis can be done for protein ligand complex? * Following are the options I have for least square fit and for RMSD calculation. MPPA is the ligand I used. Group 0 ( System) has 50085 elements Group

Re: [gmx-users] RMSD analysis and stability

On 9/15/19 7:27 AM, Bratin Kumar Das wrote: You can see the radius of gyration, number of hydrogen bond, native contact etc for assessing the stability Overall, "stability" implies persistence of important interactions (really it implies knowledge of free energy of the system, but

Re: [gmx-users] RMSD analysis and stability

You can see the radius of gyration, number of hydrogen bond, native contact etc for assessing the stability On Sun 15 Sep, 2019, 4:32 PM Quin K, wrote: > Thank you! > What else should I be looking for? > [image: mailcastr branding] Sent with Mailcastr > < >

Re: [gmx-users] RMSD analysis and stability

Thank you! What else should I be looking for? [image: mailcastr branding] Sent with Mailcastr On Sun, Sep 15, 2019 at 4:16 PM Justin Lemkul wrote: > > > On 9/15/19 5:30 AM, Quin K wrote: > > Hi everyone!

Re: [gmx-users] RMSD analysis and stability

On 9/15/19 5:30 AM, Quin K wrote: Hi everyone! I have done a MD simulation for a protein structure at 310K (100ns) this is the RMSD at around 65 ns kindly comment on the stability. Will I have to rerun the MD? Kindly let me know how to decide stability by analyzing RMSD. RMSD alone is

[gmx-users] RMSD analysis and stability

Hi everyone! I have done a MD simulation for a protein structure at 310K (100ns) this is the RMSD at around 65 ns kindly comment on the stability. Will I have to rerun the MD? Kindly let me know how to decide stability by analyzing RMSD. For backbone

Re: [gmx-users] RMSD for specified length of DNA aptamer

Hi, You should create an index file (use gmx make_ndx) that contains a list of the atom you want to perform RMSD calculation on, e.g P atoms, or whatever you want. Then when you run gmx rms, you have to pass the index file from the above step Best, On Sat, May 25, 2019 at 11:41 AM mmousivand93

[gmx-users] RMSD for specified length of DNA aptamer

Dear all I have been run molecular dynamic simulation between DNA(50bp)and small ligand,how to calculate RMSD value for specified length of DNA during 50ns simulation(for example residues from 12 to 25)? Best Regards -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] RMSD command line doubt

On 4/28/19 9:53 PM, Neena Susan Eappen wrote: Hello gromacs users, My goal is to calculate all-atom rmsd of every structure in the trajectory(.trr) to the final structure after simulation (.gro). Q1) So, I don't understand the purpose of giving .tpr input file (which was the input

[gmx-users] RMSD command line doubt

Hello gromacs users, My goal is to calculate all-atom rmsd of every structure in the trajectory(.trr) to the final structure after simulation (.gro). Q1) So, I don't understand the purpose of giving .tpr input file (which was the input structure file before production mdrun) as a structure

Re: [gmx-users] RMSD plots protein-protein complex

Moreover, this protein has ATP molecule also meaning it is a three molecule complex. On Tue, 22/1/19, Dr. Seema Mishra wrote: Subject: Re: [gmx-users] RMSD plots protein-protein complex To: gmx-us...@gromacs.org Date: Tuesday, 22 January, 2019

Re: [gmx-users] RMSD plots protein-protein complex

wrote: Subject: Re: [gmx-users] RMSD plots protein-protein complex To: gmx-us...@gromacs.org Date: Sunday, 20 January, 2019, 8:05 PM On 1/18/19 11:55 AM, marzieh gharouni wrote: > Hello > I did a simulation of protein-protein interaction with Gromacs code. In > this s

Re: [gmx-users] RMSD plots protein-protein complex

On 1/18/19 11:55 AM, marzieh gharouni wrote: Hello I did a simulation of protein-protein interaction with Gromacs code. In this simulation, the number of amino acids in each protein is about 230. The simulation production run was 300ns. After analyzing trajectory, I found that RMSD value of

[gmx-users] RMSD plots protein-protein complex

Hello I did a simulation of protein-protein interaction with Gromacs code. In this simulation, the number of amino acids in each protein is about 230. The simulation production run was 300ns. After analyzing trajectory, I found that RMSD value of protein-protein complex fluctuated near 1.8 nm but

Re: [gmx-users] RMSD plots protein-peptide complex

in Lemkul wrote: > >  Subject: Re: [gmx-users] RMSD plots protein-peptide complex >  To: gmx-us...@gromacs.org >  Date: Thursday, 10 January, 2019, 4:19 PM >  >  >  >  On 1/10/19 6:31 AM, Dr. Seema Mishra wrote: >  > >  > Thanks Justin. &g

Re: [gmx-users] RMSD plots protein-peptide complex

), then create an index group with just those atoms so you can use it for analysis. -Justin On Thu, 10/1/19, Justin Lemkul wrote: Subject: Re: [gmx-users] RMSD plots protein-peptide complex To: gmx-us...@gromacs.org Date: Thursday, 10 January

Re: [gmx-users] RMSD plots protein-peptide complex

. Otherwise, How to get that? On Thu, 10/1/19, Justin Lemkul wrote: Subject: Re: [gmx-users] RMSD plots protein-peptide complex To: gmx-us...@gromacs.org Date: Thursday, 10 January, 2019, 4:19 PM On 1/10/19 6:31 AM, Dr. Seema Mishra wrote

Re: [gmx-users] RMSD plots protein-peptide complex

On 1/10/19 6:31 AM, Dr. Seema Mishra wrote: Thanks Justin. Are these two commands for RMSD OK after making index groups for protein only? Forgive my silliness: gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o md_0_1_noPBC.xtc -pbc mol -ur compact Select 0 gmx rms -s md_0_1.tpr -f

Re: [gmx-users] RMSD plots protein-peptide complex

Thanks Justin. Are these two commands for RMSD OK after making index groups for protein only? Forgive my silliness: gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o md_0_1_noPBC.xtc -pbc mol -ur compact Select 0 gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ns

Re: [gmx-users] RMSD plots protein-peptide complex

On 1/9/19 6:07 AM, Dr. Seema Mishra wrote: Hello Any idea how to generate RMSD plots for only the protein in a protein-peptide complex? I mean, do give me commands for using only the protein backbone atoms as the g_rmsd uses all backbone atoms of peptide as well and I do not want peptide

[gmx-users] RMSD plots protein-peptide complex

Hello Any idea how to generate RMSD plots for only the protein in a protein-peptide complex? I mean, do give me commands for using only the protein backbone atoms as the g_rmsd uses all backbone atoms of peptide as well and I do not want peptide RMSD plots included. Thanks in anticipation --

Re: [gmx-users] rmsd,

I am studding phase diagram a liquid crystal (my own molecule). So I see the final structure has some ordering as I expect (as you say I should expect as scientist), but RMSD does not reach any stable value.why? So my question is can I rely on what I expect !? or I must proof the equilibrium by

Re: [gmx-users] rmsd,

On 5/31/18 1:32 PM, Amin Rouy wrote: could you please specify exactly which properties I should check? No, because this is your job as a scientist and is the kind of thing you should plan long before ever doing a simulation. What are you interested in observing? What are you testing? That

Re: [gmx-users] rmsd,

could you please specify exactly which properties I should check? because I do not have any clue of the final structure, (besides if the structure does not change, not necessarily means it is stable, maybe is it stuck in unstable phase) thanks Justin On Thu, May 31, 2018 at 7:27 PM, Justin

Re: [gmx-users] rmsd,

On 5/31/18 1:26 PM, Amin Rouy wrote: Thanks Justin. I find in some literature that RMSD is not a good parameter to specify equilibrium from it. (e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145956/). So what is the best parameter I should rely on to find the dynamic equilibrium?

Re: [gmx-users] rmsd,

Thanks Justin. I find in some literature that RMSD is not a good parameter to specify equilibrium from it. (e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145956/). So what is the best parameter I should rely on to find the dynamic equilibrium? On Thu, May 31, 2018 at 7:23 PM, Justin Lemkul

Re: [gmx-users] rmsd,

On 5/31/18 1:18 PM, Amin Rouy wrote: Hi everyone, The results of simulation show all quantities are at equilibrium, like energies, temperature, density, etc. But RMSD is increasing all the time and not reaching an equilibrium. Does it mean should I wait longer? Thermodynamic properties

[gmx-users] rmsd,

Hi everyone, The results of simulation show all quantities are at equilibrium, like energies, temperature, density, etc. But RMSD is increasing all the time and not reaching an equilibrium. Does it mean should I wait longer? thanks -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] RMSD values consideration

Try using trjconv to remove pbc before analysis Regards,Ahmed On Wed, 28 Mar, 2018 at 8:43 am, SHYANTANI MAITI wrote: Dear all, After using this command for computation of rmsd of backbone of protein protein complex consisting of three proteins :

[gmx-users] RMSD values consideration

Dear all, After using this command for computation of rmsd of backbone of protein protein complex consisting of three proteins : /home/locuz/apps/gromacs/5.1/bin/gmx_mpi rms -f md_0_1.trr -s md_0_1.tpr The rmsd is drastically increasing from 1 to 6 nm and after that it again decreases to 1nm. can

Re: [gmx-users] RMSD in Angstrom

​Hi, This is more of a xmgrace related issue. Gromacs' length units have always been nm and there's no way to "ask" for different units. Now you either modify the file yourself (manually or with a simple awk one-liner) or ask the plotting program to convert the units. I don't know about xmgrace,

Re: [gmx-users] RMSD in Angstrom

Hi, Not in GROMACS. You can edit the file to work however you want, however. Mark On Mon, Oct 23, 2017 at 9:57 AM Roshan Shrestha wrote: > Hi, > The default unit for RMSD in gromacs is in nanometer (nm). Are there > any options available in gromacs so that I can have

[gmx-users] RMSD in Angstrom

Hi, The default unit for RMSD in gromacs is in nanometer (nm). Are there any options available in gromacs so that I can have rmsd values in Angstrom while plotting it in xmgrace. Thanks -- Roshan Shrestha M.Sc (Physics) Central Department of Physics, Tribhuvan University Kathmandu, Nepal --

[gmx-users] RMSD value

Dear users, I have a question regarding the calculation of RMSD value for a big system comprising of many replicas of the same peptide. I know that with RMSD fit you can choose to “superimpose” your reference structure to the one from the trajectory (rot+trans). My question is when supplying

[gmx-users] RMSD

Dear All, If I want to show difference in RMSD of peptide conformations in different solution compositions, what should I choose as reference structure so that more representative figure is formed? The .tpr file that I should choose for reference structure should be the file after equilibration

[gmx-users] RMSD output from gmx confrms differs from gmx rms?

Hello: I would like to measure the C RMSDs between structures from a trajectory and a PDB structure. With gmx rms, I get warning messages about different number of atoms in the input files. So I create pdb files from the trajectory, with solvent excluded. But when I run gmx confrms with these

Re: [gmx-users] RMSD analysis

On 6/6/17 4:01 PM, RAHUL SURESH wrote: Dear Justin I think I have confused so much. Let me try to put it in simple way. 1.Can I compare Rmsd , rg , rmsf of protein-ligand complex with that of monomer(just protein) to explain stability? RMSD may be an indicator of something going on but by

Re: [gmx-users] RMSD Matrix Error

which > frames to use? > > > > Message: 2 > Date: Mon, 05 Jun 2017 01:37:37 + > From: Mark Abraham <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] RMSD Matrix error > Message-ID: >

Re: [gmx-users] RMSD analysis

Dear Justin I think I have confused so much. Let me try to put it in simple way. 1.Can I compare Rmsd , rg , rmsf of protein-ligand complex with that of monomer(just protein) to explain stability? 2. Time step of monomer(just protein) simulation is 150ns and protein-ligand complex is 50ns. In

Re: [gmx-users] RMSD analysis

On 6/6/17 1:11 PM, RAHUL SURESH wrote: Dear Justin Thank you. I am considering Rmsd rmsf rg as just supplementary analysis for my study. My aim to analyse conformational change in protein. I would like to bring a note on protein stability after ligand binding. I don't know to which part of

Re: [gmx-users] RMSD analysis

Dear Justin Thank you. I am considering Rmsd rmsf rg as just supplementary analysis for my study. My aim to analyse conformational change in protein. I would like to bring a note on protein stability after ligand binding. I don't know to which part of monomer I can compare the rmsd of complex

Re: [gmx-users] RMSD analysis

On 6/6/17 2:12 AM, RAHUL SURESH wrote: Dear Users *Exp procedure:* I have simulated the protein monomer for 150ns. Using the 150ns conformer, ligand is docked to the protein using autodock and the simulation is carried out for 50ns. *Analysis:* Is it possible to compare my RMSD, RMSF, ROG

Re: [gmx-users] RMSD Matrix Error

? Message: 2 Date: Mon, 05 Jun 2017 01:37:37 + From: Mark Abraham <mark.j.abra...@gmail.com> To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] RMSD Matrix error Message-ID:

[gmx-users] RMSD analysis

Dear Users *Exp procedure:* I have simulated the protein monomer for 150ns. Using the 150ns conformer, ligand is docked to the protein using autodock and the simulation is carried out for 50ns. *Analysis:* Is it possible to compare my RMSD, RMSF, ROG analysis of complex system with that of

Re: [gmx-users] RMSD Matrix error

Hi, On Sun, Jun 4, 2017 at 4:08 PM Apramita Chand wrote: > Dear All, > > When I'm trying to construct a RMSD matrix , using the command > g_rms -s protein_equili.gro -f protein_model1_ut.xtc -m > rmsd-matrix.xpm -tu ns > > I get the error: > Last frame

[gmx-users] RMSD Matrix error

Dear All, When I'm trying to construct a RMSD matrix , using the command g_rms -s protein_equili.gro -f protein_model1_ut.xtc -m rmsd-matrix.xpm -tu ns I get the error: Last frame 20 time 20.000 Building RMSD matrix, 21x21 elements element 28982; time 2.90 Killed I

[gmx-users] rmsd value from g_cluster

Hi, I have a .xtc file with 1000 frames and I want to use g_cluster to generate the rmsd value between each two frames in the xtc file. However, I cannot find the exact rmsd values in the .xpm file generated by g_cluster. PS, I use gromacs 4.6.5 Hui -- Gromacs Users mailing list *

Re: [gmx-users] RMSD of energy minimized structure

Hi Surya, The first part ss a warning, not an error. It also says (implicitly) that if the molecules are not broken across PBC then there's nothing to worry about whatsoever. So just assert that your molecules are not split over PBC. Have a look at the trajectory. If there are frames with one

[gmx-users] RMSD of energy minimized structure

Dear gromacs users, I have done energy minimization of clustered PDBs. When I try to calculate the RMSD between the minimized clustered PDB and the starting structure of MD simulations I got the following warning. If there are molecules in the input tarjectory file that are broken across

Re: [gmx-users] RMSD of interested region?

Create two index groups. One with 28-197 residues and second group with 2-27. Supply this index file to gmx rms (if using 5.1) with -n option and select 28-197 as fit group and 2-27 for RMSD analysis. Regards, Sarath On 20 September 2016 at 12:05, Seera Suryanarayana

[gmx-users] RMSD of interested region?

Dear gromcas users, I have done simulations for 100ns for protein of my interest. The protein length is 197 residues and I fixed the positions one n-terminal residue and from 28th residue to 197 residues also fixed. My interest of area in protein is from 2 to 27 residues. Although I have done

Re: [gmx-users] RMSD question

Hi Teresa, You probably want to try clustering, and then check the percentage of bound/unbound structures in the clusters you get. Just the RMSD won't tell you much. Cheers, Tsjerk On Wed, Jun 8, 2016 at 11:30 AM, ingram wrote: > Dear GROMACS community, > > I am

[gmx-users] RMSD question

Dear GROMACS community, I am trying to identify the number of unique peptide structures on the surface of a slab. If I simply calculate the RMSD between the protein atoms in each frame of the trajectory this tells me nothing about how these structures compare on the surface as the constraint

Re: [gmx-users] RMSD calculation of protein-ligand complex

Hi Aswathy You can make a group with Protein and ligand in an index file using make_ndx and pass it with -n in gmx rms. Ashutosh On Fri, Apr 22, 2016 at 6:46 PM, Aswathy soman wrote: > Hi, > I have done a 100 ns simulation of protein-ligand complex. I was wondering

Re: [gmx-users] RMSD calculation of protein-ligand complex

You can make an index group with both protein+ligand using make_ndx command and use the index file from make_ndx to run the rmsd analysis Regards, Sarath -- Sarath Chandra Dantu, PhD, ELS Room No. 606, New BSBE Building Department of Biosciences and Bioengineering Indian Institute of

Re: [gmx-users] RMSD calculation of protein-ligand complex

Hi, You can create a group with the protein and the ligand using the make_ndx tool. Then you can use the created index file as input for your rmsd calculation. Cheers, On 22 Apr 2016 10:47, "Aswathy soman" wrote: > Hi, > I have done a 100 ns simulation of

Re: [gmx-users] RMSD calculation of protein-ligand complex

Hi, You must create a new índex group using make_ndx. Regards Pedro Lacerda Em 22/04/2016 06:47, "Aswathy soman" escreveu: > Hi, > I have done a 100 ns simulation of protein-ligand complex. I was wondering > is it possible to calculate RMSD of the entire

[gmx-users] RMSD calculation of protein-ligand complex

Hi, I have done a 100 ns simulation of protein-ligand complex. I was wondering is it possible to calculate RMSD of the entire protein-ligand complex. How to select the complex as such during the calculation of RMSD because there is no group as protein+ligand. Thanking you in advance Regards,

Re: [gmx-users] Rmsd Problem

There is no attachment i can see. BTW from literature and knowledge in your typical problem will help to analyse results. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] Rmsd Problem

Deaer Gromacs users, I have a problem in analyzing my MD simulation results of RMSD the graph of apo protein lies below while the graph lines of ligand bound complexes lies above.I am not getting what this graph is showing. Kindly give me some clues to interpret this graph. Here I am attaching

Re: [gmx-users] RMSD plot of the backbone atoms

On 3/3/16 7:01 AM, Mahboobeh Eslami wrote: hi GMX usersi have done MD simulation for a protein-protein complex. i want to get RMSD plot of the backbone atoms for one of the protein chain. how do i prepare index file?thanks for your help Use make_ndx. Type "help" at the prompt if you

[gmx-users] RMSD plot of the backbone atoms

hi GMX usersi have done MD simulation for a  protein-protein complex.  i want to get RMSD plot of the backbone atoms for one of the  protein chain. how do i prepare index file?thanks for your help -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] RMSD reproducibility

On 2/15/16 12:21 PM, Biplab Ghosh wrote: Dear Gromacs Users, I have the following question: Suppose I repeat a simulation, keeping everything exactly the same. What will happen to RMSD? Will it be exactly same with the previous run? No. If not, then how much variation is expected?

[gmx-users] RMSD reproducibility

Dear Gromacs Users, I have the following question: Suppose I repeat a simulation, keeping everything exactly the same. What will happen to RMSD? Will it be exactly same with the previous run? If not, then how much variation is expected? To check this, I ran two independent simulations: 1) upto

[gmx-users] RMSD comparison to a different reference structure.

Hi, I was wondering if you would be able to advise me of the best method to compare a mutated and WT structure. I was hoping to perform RMSD analysis for certain regions within a mutation against the same region within the wild type structure. Unfortunately, the atom numbering is likely to

Re: [gmx-users] RMSD comparison to a different reference structure.

: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Erik Marklund [erik.markl...@chem.ox.ac.uk] Sent: 07 September 2015 11:42 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] RMSD comparison to a different reference structure. Hi, How

Re: [gmx-users] RMSD comparison to a different reference structure.

Hi, How about comparing only C-alphas? As long as you have the same number of residues, that should work. You need to make reduced versions of your tpr and trajectory files. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of

[gmx-users] RMSD distribution calculation using g_cluster

During calculation of RMSD distribution using *g_cluster*, the Y axis of the XVG file showing the RMSD distribution denotes a.u. i.e arbitrary unit which I think probably the frequency. But it is not clear which frequency it exactly is and also kindly let me know how the calculation happened. --

Re: [gmx-users] RMSD between two groups

Hi, How about using g_dist and using an index file?! Cheers Mohsen On Mon, Mar 23, 2015 at 6:50 PM, leila salimi leilasal...@gmail.com wrote: Dear all, I have a question regarding to analyse the trajectory that I have. I am studying the interaction of peptide at interfaces, e.g Oxygen of

[gmx-users] RMSD between two groups

Dear all, I have a question regarding to analyse the trajectory that I have. I am studying the interaction of peptide at interfaces, e.g Oxygen of carboxylate group of side chains with Cations at the interface! I would like to calculate the distance between Oxygen of carboxylate group of side

[gmx-users] RMSD graph over time and g_cluster RMSD distribution seem at odds with each other

Dear Gromacs users, I am analyzing the RMSD evolution of a trajectory with g_rms and clustering it with g_cluster (GROMOS, cutoff 0.1). I am noticing something quite odd in the RMSD distribution. I link here the RMSD evolution over time , the cluster ID over time, and the RMSD distribution

Re: [gmx-users] RMSD graph over time and g_cluster RMSD distribution seem at odds with each other

Hi Massimo, You have two clusters, both with low within-cluster RMSD. This shows up as the first peak in the RMSD distribution. The second peak is the between-clusters RMSD. Cheers, Tsjerk On Wed, Aug 13, 2014 at 3:14 PM, ms deviceran...@gmail.com wrote: Dear Gromacs users, I am

Re: [gmx-users] RMSD graph over time and g_cluster RMSD distribution seem at odds with each other

Hi Tsjerk, On 8/13/14 3:19 PM, Tsjerk Wassenaar wrote: You have two clusters, both with low within-cluster RMSD. This shows up as the first peak in the RMSD distribution. The second peak is the between-clusters RMSD. I am sorry, but I don't understand anything here - what does within-cluster

Re: [gmx-users] RMSD graph over time and g_cluster RMSD distribution seem at odds with each other

H Massimo, The RMSD over time is the RMSD against a single reference structure. For clustering you use the RMSD matrix, which has all pairwise RMSDs. The distribution you show is the distribution of RMSD values in that matrix. Cheers, Tsjerk On Wed, Aug 13, 2014 at 3:44 PM, ms

Re: [gmx-users] RMSD graph over time and g_cluster RMSD distribution seem at odds with each other

On 8/13/14 4:01 PM, Tsjerk Wassenaar wrote: H Massimo, The RMSD over time is the RMSD against a single reference structure. For clustering you use the RMSD matrix, which has all pairwise RMSDs. The distribution you show is the distribution of RMSD values in that matrix. Aha! This makes much

Re: [gmx-users] RMSD graph over time and g_cluster RMSD distribution seem at odds with each other

On 8/13/14, 10:11 AM, ms wrote: On 8/13/14 4:01 PM, Tsjerk Wassenaar wrote: H Massimo, The RMSD over time is the RMSD against a single reference structure. For clustering you use the RMSD matrix, which has all pairwise RMSDs. The distribution you show is the distribution of RMSD values in

Re: [gmx-users] RMSD graph over time and g_cluster RMSD distribution seem at odds with each other

On 8/13/14 4:17 PM, Justin Lemkul wrote: Aha! This makes much more sense then, thanks! Is there a Gromacs command to get the histogram of RMSD against a single reference structure, then? You can construct histograms of any time series with g_analyze -dist. OK, I forgot that. Thanks a lot,

[gmx-users] RMSD

Dear gromacs users Can somebody tell me how to calculate the RMSD of the peptide conformation relative to the NMR structure? Best wishes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] RMSD per residue

On 12/19/13 6:03 AM, Saman Shahriyari wrote: Dear users I am trying to have the RMSD per residue profile of my trajectory. i approached this by using g_rmsf tool with -od and -res options. although i can have such profile, but it seems that the average structure of my trajectory is being