Re: [gmx-users] RMSD

On 5/5/13 12:40 PM, Shima Arasteh wrote: Hi, I' like to know if it is possible to get the average RMSD through g_rms command? Or I need to get it manually? Use g_analyze. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochem

[gmx-users] RMSD

Hi, I' like to know if it is possible to get the average RMSD through g_rms command? Or I need to get it manually? Thanks for your suggestions. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

Re: [gmx-users] RMSD from the average structure

Dear Sir, Thanks for the useful insight. On Fri, Apr 26, 2013 at 2:21 PM, Erik Marklund wrote: > Average coordinates are problematic and not generally representative. > Consider for instance the average coordinates of a methyl group connected > to X. The rotation around the C-X bond causes the

Re: [gmx-users] RMSD from the average structure

Average coordinates are problematic and not generally representative. Consider for instance the average coordinates of a methyl group connected to X. The rotation around the C-X bond causes the average positions of the hydrogens to line up. Consider using g_cluster to find representative structu

Re: [gmx-users] RMSD from the average structure

Thanks for your reply. Actually I am interested to see how much structural deviation is occurring in a protein during the simulation from its average position of atoms rather than the initial position (crystal structure or starting structure). The motivation of doing this analysis is the fact that

Re: [gmx-users] RMSD from the average structure

Hi Bipin Singh, That indeed gives you the RMSD against the average. Do think about it a bit more: do you want the average of the whole structure, or should you account for a phase of relaxation? Cheers, Tsjerk On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul wrote: > > > On 4/24/13 3:06 AM, bi

Re: [gmx-users] RMSD from the average structure

On 4/24/13 3:06 AM, bipin singh wrote: Hi all, Please let me know whether this is the right way to calculate RMSD from the average structure from a simulation: g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg average.pdb: is the pdb file produced using -ox option of g_rmsf. You can calcu

[gmx-users] RMSD from the average structure

Hi all, Please let me know whether this is the right way to calculate RMSD from the average structure from a simulation: g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg average.pdb: is the pdb file produced using -ox option of g_rmsf. -- *--- Thanks and Regards, Bipin Sin

Re: [gmx-users] RMSD

TE: 54 011 4964-8273 De: Shima Arasteh Para: Discussion list for GROMACS users Enviado: miércoles, 23 de enero de 2013 16:14 Asunto: Re: [gmx-users] RMSD What I see in xvg file is as below: # g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg # # g_rms is part o

Re: [gmx-users] RMSD

my purposed conformers?  Thanks for all your suggestions. Sincerely, Shima From: Leandro Bortot To: Discussion list for GROMACS users Sent: Thursday, January 24, 2013 8:54 PM Subject: Re: [gmx-users] RMSD      you can make a simple script which calculates

Re: [gmx-users] RMSD

73 > > > > De: Shima Arasteh > Para: Discussion list for GROMACS users > Enviado: miércoles, 23 de enero de 2013 16:14 > Asunto: Re: [gmx-users] RMSD > > What I see in xvg file is as below: > > # g_rms -s 1.pdb -f 2.pdb -o rmsd1.x

Re: [gmx-users] RMSD

Asunto: Re: [gmx-users] RMSD What I see in xvg file is as below: # g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg # # g_rms is part of G R O M A C S: # # Gromacs Runs On Most of All Computer Systems # @    title "RMSD" @    xaxis  label "Time (ps)" @    yaxis  label "RMSD

Re: [gmx-users] RMSD

On 1/23/13 1:14 PM, Shima Arasteh wrote: What I see in xvg file is as below: # g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg # # g_rms is part of G R O M A C S: # # Gromacs Runs On Most of All Computer Systems # @title "RMSD" @xaxis label "Time (ps)" @yaxis label "RMSD (nm)" @TYPE xy @ su

Re: [gmx-users] RMSD

: Justin Lemkul To: Discussion list for GROMACS users Cc: Sent: Wednesday, January 23, 2013 9:36 PM Subject: Re: [gmx-users] RMSD On 1/23/13 12:48 PM, Shima Arasteh wrote: > I want to find the structure with the lowest RMSD, so I think it does not > make different to set any of pdb files

Re: [gmx-users] RMSD

On 1/23/13 12:48 PM, Shima Arasteh wrote: I want to find the structure with the lowest RMSD, so I think it does not make different to set any of pdb files as the ref structure. I made an attempt and got the RMSD regarding the first pdb file. The RMSD relative to -1 for the ref structure, is w

Re: [gmx-users] RMSD

correct? Thanks for your suggestions.   Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Wednesday, January 23, 2013 7:20 PM Subject: Re: [gmx-users] RMSD On 1/23/13 10:38 AM, Shima Arasteh wrote: > >

Re: [gmx-users] RMSD

I think what you really need is not Gromacs. For example, you can use UCSF Chimera to get alignment and RMSD between two PDBs. dawei On Wed, Jan 23, 2013 at 10:38 AM, Shima Arasteh wrote: > > > Hi, > > Is it possible to get RMSD of 10 different pdb files by GROMACS? > g_rms may help? > > >

Re: [gmx-users] RMSD

On 1/23/13 10:38 AM, Shima Arasteh wrote: Hi, Is it possible to get RMSD of 10 different pdb files by GROMACS? Relative to what? Each other? Some universal reference? g_rms may help? That, or g_confrms, depending on what you're actually trying to measure. -Justin -- =

[gmx-users] RMSD

Hi, Is it  possible to get RMSD of 10 different pdb files by GROMACS? g_rms may help? Sincerely, Shima  -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search bef

Re: [gmx-users] RMSD plot

On 30/07/2012 4:49 PM, tarak karmakar wrote: Dear Mark, Thanks for the reply. But one thing I am just wondering is that while calculating the RMSD, I'm considering the backbone only. So I can take the initial pdb file as reference for the trajectory. While doing so I see the RMSD graph is conti

Re: [gmx-users] RMSD plot

Dear Mark, Thanks for the reply. But one thing I am just wondering is that while calculating the RMSD, I'm considering the backbone only. So I can take the initial pdb file as reference for the trajectory. While doing so I see the RMSD graph is continuing to increase and not getting equilibrium v

Re: [gmx-users] RMSD plot

On 30/07/2012 3:39 AM, tarak karmakar wrote: Dear All, In my initial protein pdb structure I have added some external ligand molecules and as a result of that there are several short contacts. So, well, I minimized the system and then got the 'prot_min.gro' file. Now after the equilibration run,

[gmx-users] RMSD plot

Dear All, In my initial protein pdb structure I have added some external ligand molecules and as a result of that there are several short contacts. So, well, I minimized the system and then got the 'prot_min.gro' file. Now after the equilibration run, I plotted the RMSD of the resulting trajectory

Re: [gmx-users] RMSD analysis during production MD

Acoot Brett wrote: Dear All, During a 1 ns production analysis (before it completes), I can analysis the RMSD by "g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns" without influence the normal calculation of the production analysis, right? It's always safer to make a copy of

[gmx-users] RMSD analysis during production MD

 Dear All,   During a 1 ns production analysis (before it completes), I can analysis the RMSD by "g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns" without influence the normal calculation of the production analysis, right?   Cheers,   Acoot   -- gmx-users mailing listgmx-users@gr

Re: [gmx-users] RMSD sudden jump

Sorry I realized I attached the .xvg. Here is a png for a easier visualization. Sorry for the inconvenience. Thanks, Davide 2012/3/14 Davide Mercadante > Hi Tsjerk, > > thanks very much for your prompt reply. > I checked the last 5ns rmsd against an average structure calculated in the > same t

Re: [gmx-users] RMSD sudden jump

Hi Tsjerk, thanks very much for your prompt reply. I checked the last 5ns rmsd against an average structure calculated in the same time range and effectively the system seems to be converging (I attached the graph). However, the switch seems unlikely as the protein seems to lose part of its fold.

Re: [gmx-users] RMSD sudden jump

Hi Davide, If you've checked the trajectory, and you've assured that there are no atoms wrapping over the periodic boundaries, and you've noticed a sudden change in conformation, then probably that's what it is: a sudden change in conformation. That does agree with the plot. After a rather station

[gmx-users] RMSD sudden jump

Dear gromacs users, I have performed ~30ns MD on a protein in TIP4P water using the OPLS forcefield. I have concatenated the trajectories for each step using trjcat and removed pbc effects using pbc nojump. All the particles of the system now don't jump anymore and the molecule doesn't appear as

Re: [gmx-users] RMSD value

On 9/01/2012 8:26 PM, madhumita das wrote: Hi GROMACS Users, I have simulated a protein(pdb id 3D9S) for 5 nanoseconds. This protein contains 978 residues and after 5 nanoseconds I got 2.35 by comparing pdb structure with simulated one. I want to know is this

[gmx-users] RMSD value

Hi GROMACS Users, I have simulated a protein(pdb id 3D9S) for 5 nanoseconds. This protein contains 978 residues and after 5 nanoseconds I got 2.35 by comparing pdb structure with simulated one. I want to know is this value is ok or protein is disrupted? Yours f

Re: [gmx-users] RMSD

anluca.sant...@ibs.fr > Fecha: 15-nov-2011 10:18 > Para: "Discussion list for GROMACS users" > Asunto: Re: [gmx-users] RMSD > > > On 11/15/11 8:23 PM, shahid nayeem wrote: > > Dear all > I am interested to get contour plot of residue RMSD vs time graph. I want &g

Re: [gmx-users] RMSD

. regards Felipe Mensaje original De: gianluca.sant...@ibs.fr Fecha: 15-nov-2011 10:18 Para: "Discussion list for GROMACS users" Asunto: Re: [gmx-users] RMSD On 11/15/11 8:23 PM, shahid nayeem wrote: Dear all I am interested to get contour plot of residue RMSD vs time

Re: [gmx-users] RMSD

On 11/15/11 8:23 PM, shahid nayeem wrote: Dear all I am interested to get contour plot of residue RMSD vs time graph. I want to get the flexible and rigid regions of protein chain during simulation. g_rmsf does not gives me this plot. Please help shahid Nayeem Try g_rmsf -res , it could be

[gmx-users] RMSD

Dear all I am interested to get contour plot of residue RMSD vs time graph. I want to get the flexible and rigid regions of protein chain during simulation. g_rmsf does not gives me this plot. Please help shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mai

Re: [gmx-users] RMSD bonds and angles

Hey :) If that is what you want, you'll have to turn to programming. But what do you think to gain from it? First get to the bottom of things you can do with gromacs already. Then, if the tools available don't help in answering your question, think of what you'd need to get it done. Cheers, Tsje

Re: [gmx-users] RMSD bonds and angles

No, it calculates with respect to the positions atom. but I want to calculate the RMSD bonds (A˚ ) and RMSD angles (o). 2011/10/4 Mark Abraham > On 4/10/2011 7:05 PM, ahmet yıldırım wrote: > > any hints? :( > > > You didn't find something useful in the section titled "Root mean square > deviati

Re: [gmx-users] RMSD bonds and angles

On 4/10/2011 7:05 PM, ahmet y?ld?r?m wrote: any hints? :( You didn't find something useful in the section titled "Root mean square deviations in structure"? Mark 03 Ekim 2011 22:32 tarihinde ahmet y?ld?r?m > yazd?: I look at chapter 8 but I didnt found tha

Re: [gmx-users] RMSD bonds and angles

any hints? :( 03 Ekim 2011 22:32 tarihinde ahmet yıldırım yazdı: > I look at chapter 8 but I didnt found that I want. can you give a hint? > Thanks > > > 2011/10/3 Mark Abraham > >> On 3/10/2011 10:29 PM, ahmet yıldırım wrote: >> >>> Dear users, >>> >>> How can I calculate the RMSD bonds (A˚ )

Re: [gmx-users] RMSD bonds and angles

I look at chapter 8 but I didnt found that I want. can you give a hint? Thanks 2011/10/3 Mark Abraham > On 3/10/2011 10:29 PM, ahmet yıldırım wrote: > >> Dear users, >> >> How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)? >> > > Please start your search in chapter 8 of the manual, an

Re: [gmx-users] RMSD bonds and angles

On 3/10/2011 10:29 PM, ahmet yıldırım wrote: Dear users, How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)? Please start your search in chapter 8 of the manual, and consider doing some tutorial material. Someone is likely to have covered some similar procedures. Mark -- gmx-user

[gmx-users] RMSD bonds and angles

Dear users, How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search

Re: [gmx-users] RMSD with Vsite vs No Vsites

On 6/05/2011 5:32 PM, Sikandar Mashayak wrote: well the deviations are about more than 0.5 nm.. And what does gmxcheck -s1 -s2 show? Mark On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai > wrote: On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote: > Hi >

Re: [gmx-users] RMSD with Vsite vs No Vsites

well the deviations are about more than 0.5 nm.. On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai wrote: > On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote: > > Hi > > > > As a test case, I did two simulations one the usual Protein in Water and > other with Vsites at COM of each monomer but t

Re: [gmx-users] RMSD with Vsite vs No Vsites

On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote: > Hi > > As a test case, I did two simulations one the usual Protein in Water and > other with Vsites at COM of each monomer but these Vsites dont interact with > anyone else. I was expecting results of these two should match almost > exa

Re: [gmx-users] RMSD with Vsite vs No Vsites

On 6/05/2011 2:21 AM, Sikandar Mashayak wrote: Hi As a test case, I did two simulations one the usual Protein in Water and other with Vsites at COM of each monomer but these Vsites dont interact with anyone else. I was expecting results of these two should match almost exactly, but when I com

[gmx-users] RMSD with Vsite vs No Vsites

Hi As a test case, I did two simulations one the usual Protein in Water and other with Vsites at COM of each monomer but these Vsites dont interact with anyone else. I was expecting results of these two should match almost exactly, but when I compare the rmsd for Protein there seems to be discrepa

Re: [gmx-users] RMSD Calculation

Hey :) You probably want to fit on the protein and calculate the RMSD on the ligand. You may need to specify these groups in an index file. Hope it helps, Tsjerk On Mar 27, 2011 3:28 AM, "Justin A. Lemkul" wrote: Nancy wrote: > > Hi All, > > I need to determine the RMSD of a small molecule co

Re: [gmx-users] RMSD Calculation

Nancy wrote: Hi All, I need to determine the RMSD of a small molecule cocrystallized ligand, against a large number of predicted docked conformations. Please let me know what is the best method for doing this. I answered this yesterday: http://lists.gromacs.org/pipermail/gmx-users/2011

[gmx-users] RMSD Calculation

Hi All, I need to determine the RMSD of a small molecule cocrystallized ligand, against a large number of predicted docked conformations. Please let me know what is the best method for doing this. Thank you very much, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

Re: [gmx-users] RMSD truncation Restart simulation problems

Henri Mone wrote: Hi Mark, Thanks for your feedback. The simulations are running now again. I got one questions, I think it will be also of interest for the others on the mailinglist. I used "grompp" with the "-t state0.cpt" option, are the starting velocities taken from the cpt files or are

Re: [gmx-users] RMSD truncation Restart simulation problems

Hi Mark, Thanks for your feedback. The simulations are running now again. I got one questions, I think it will be also of interest for the others on the mailinglist. I used "grompp" with the "-t state0.cpt" option, are the starting velocities taken from the cpt files or are the assigned randomly

Re: [gmx-users] RMSD truncation Restart simulation problems

On 8/03/2011 9:41 PM, Henri Mone wrote: Hi All, hi Mark, Here are some more details. The outputs and error messages are attached at the end of the e-mail. After truncation I get the error message [1a], gromacs has problems with the checksum of the trr fles. After truncation the trajectories (xtc,

Re: [gmx-users] RMSD truncation Restart simulation problems

Hi All, hi Mark, Here are some more details. The outputs and error messages are attached at the end of the e-mail. After truncation I get the error message [1a], gromacs has problems with the checksum of the trr fles. After truncation the trajectories (xtc, trr) have the same length of 27752 frames

Re: [gmx-users] RMSD truncation Restart simulation problems

On 7/03/2011 8:23 PM, Henri Mone wrote: Dear Gromacs Users/ Experts and Beginners, I'm using Gromacs 4.5.3 to run REMD simulation. The REMD simulations stooped abruptly and therefore the replicas have uneven information. One of the checkpoint differ in time and frame compared to other replicas.

[gmx-users] RMSD truncation Restart simulation problems

Dear Gromacs Users/ Experts and Beginners, I'm using Gromacs 4.5.3 to run REMD simulation. The REMD simulations stooped abruptly and therefore the replicas have uneven information. One of the checkpoint differ in time and frame compared to other replicas. My case is very similar to the problem re

Re: [gmx-users] RMSD and Resolution

Hi Ahmet, I'm not sure whether it's been checked. It has been found that NMR structures tend to yield larger deviations than crystal structures. If you're going to try, due make sure to compensate for other potential influences, such as the size and sphericity of the proteins. Cheers, Tsjerk 20

[gmx-users] RMSD and Resolution

Hi, Is there a relationship between RMSD value obtained from the calculation and Resolution value in PDB file? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gro

Re: [gmx-users] rmsd between different monomers

On 9/05/2010 10:01 PM, Anupam Nath Jha wrote: Ok. But when I run this command g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out it ask me groups... and that i thought is for fitting/// for example - Select group for least squares fit Group 0 (C-alpha_chain1)

Re: [gmx-users] rmsd between different monomers

you said you have used online server for superimposition ... which one you used... try TOPMATCH server On Sun, May 9, 2010 at 5:31 PM, Anupam Nath Jha wrote: > > Ok. > > But when I run this command > g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out > > it ask me groups... and that i tho

Re: [gmx-users] rmsd between different monomers

Ok. But when I run this command g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out it ask me groups... and that i thought is for fitting/// for example - Select group for least squares fit Group 0 (C-alpha_chain1) has 249 elements Group 1 (C-alpha_chain2)

Re: [gmx-users] rmsd between different monomers

On 9/05/2010 9:29 PM, Justin A. Lemkul wrote: Anupam Nath Jha wrote: Anupam Nath Jha wrote: Dear all I made an index file with 4 different groups for 4 different chains (since my protein is a tetramer) and then run g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out to get the rmsd bet

Re: [gmx-users] rmsd between different monomers

Anupam Nath Jha wrote: Anupam Nath Jha wrote: Dear all I made an index file with 4 different groups for 4 different chains (since my protein is a tetramer) and then run g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out to get the rmsd between two different monomers from the same struc

Re: [gmx-users] rmsd between different monomers

> > > Anupam Nath Jha wrote: >> Dear all >> >> I made an index file with 4 different groups for 4 different chains (since my >> protein is a tetramer) and then run >> >> g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out >> >> to get the rmsd between two different monomers from the same struct

Re: [gmx-users] rmsd between different monomers

Itamar Kass wrote: Hi Anupam , To me it seems that you have used the the wrong groups for the RMSD, you actually compare the protein to himself. Have a second look on at the group contact, you groups should be numbered 12 or higher. Not in this case. The headers of the .xvg file in the ori

Re: [gmx-users] rmsd between different monomers

Anupam Nath Jha wrote: Dear all I made an index file with 4 different groups for 4 different chains (since my protein is a tetramer) and then run g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out to get the rmsd between two different monomers from the same structure, it asked me two dif

Re: [gmx-users] rmsd between different monomers

toria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@med.monash.edu.au - Original Message - From: Anupam Nath Jha Date: Sunday, May 9, 2010 3:48 pm Subject: [gmx-users] rmsd between different monomers To:

[gmx-users] rmsd between different monomers

Dear all I made an index file with 4 different groups for 4 different chains (since my protein is a tetramer) and then run g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out to get the rmsd between two different monomers from the same structure, it asked me two different groups and I gave 0

Re: [gmx-users] rmsd between different monomers

On 7/05/2010 7:11 PM, Anupam Nath Jha wrote: Dear all How can we calculate the rmsd between different monomers from of a protein. for example I have a tetramer and I have to calculate the rmsd between chain A to B, A to C and A to D with time. I was trying using g_rms but couldn't do that. g

Re: [gmx-users] rmsd between different monomers

There is one web-server in our lab. http://10.188.1.15/3dss/ Use third option. On Fri, May 7, 2010 at 2:41 PM, Anupam Nath Jha wrote: > > Dear all > > How can we calculate the rmsd between different monomers from of a protein. > for > example I have a tetramer and I have to calculate the rmsd bet

[gmx-users] rmsd between different monomers

Dear all How can we calculate the rmsd between different monomers from of a protein. for example I have a tetramer and I have to calculate the rmsd between chain A to B, A to C and A to D with time. I was trying using g_rms but couldn't do that. thanks with regards anupam -- Science is facts

Re: [gmx-users] RMSD of Different Simulations

g_confrms -f1 conf1.gro -f2 conf2.gro -n1 ind1.ndx -n2 ind2,ndx should do the trick. On Feb 9, 2010, at 1:27 AM, Mark Abraham wrote: On 09/02/10 10:20, V Hariharan wrote: Hello All, I've taken the average peptide structure from two different MD simulations using g_rmsf. Is there a method

Re: [gmx-users] RMSD of Different Simulations

On 09/02/10 10:20, V Hariharan wrote: Hello All, I've taken the average peptide structure from two different MD simulations using g_rmsf. Is there a method for calculating the RMSD between those two structures? The only difference between the two peptides is a single residue mutation. Thanks.

[gmx-users] RMSD of Different Simulations

Hello All, I've taken the average peptide structure from two different MD simulations using g_rmsf. Is there a method for calculating the RMSD between those two structures? The only difference between the two peptides is a single residue mutation. Thanks. --Venk

Re: [gmx-users] rmsd value discrepancy from g_rms & g_cluster

Segun Jung wrote: Hello there, I have used g_rms and g_cluster for RNA structure analysis and noticed that they give me different rmsd values. For example, calculating rmsd values using the g_rms gives me a minimum rmsd value of 0.7nm, but using g_cluster it gives me the minimum rmsd val

[gmx-users] rmsd value discrepancy from g_rms & g_cluster

Hello there, I have used g_rms and g_cluster for RNA structure analysis and noticed that they give me different rmsd values. For example, calculating rmsd values using the g_rms gives me a minimum rmsd value of 0.7nm, but using g_cluster it gives me the minimum rmsd value of 0.3nm. Both uses th

Re: [gmx-users] RMSD

leila karami wrote: Hi I have 2 questions about rmsd calculation: 1) why rmsd calculation is done on heavy atoms? 2) what means of mass weighted superposition (rmsd is calculated after mass weighted superposition) Consider the difference between centre of mass and center of geometry...

Re: [gmx-users] RMSD

On 1/10/10 3:51 AM, leila karami wrote: Hi I have 2 questions about rmsd calculation: 1) why rmsd calculation is done on heavy atoms? You calculate RMSD on whatever subset of atoms you wish; you are not necessarily limited to heavy atoms only. 2) what means of mass weighted superposition

[gmx-users] RMSD

Hi I have 2 questions about rmsd calculation: 1) why rmsd calculation is done on heavy atoms? 2) what means of mass weighted superposition (rmsd is calculated after mass weighted superposition) Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.g

[gmx-users] rmsd vs residue no

dear Tsjerk your word is true but how should be changed index file? I don't know. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe reques

Re: [gmx-users] RMSD Vs Residue no by Grace

Hi, RMSD is given at a specific time, so you can ran g_rms for each residue (create index file witha specific residue in) and then take the RMSD of each residue at time T and plot it. But I think you should look into g_rmsf, this might fit you better, although it calculate the fluctuations rather

Re: [gmx-users] RMSD Vs Residue no by Grace

rituraj purohit wrote: Dear friends, I am able to plot, RMSD between Time (ps) by following command by using GRACE.. g_rms -s md.tpr -f md.xtc xmgrace rmsd.xvg How we can I plot a graph betwwen RMSD and residue no ..?? My aim is to find RMSD at each residues. How i can do that? g_rm

[gmx-users] RMSD Vs Residue no by Grace

Dear friends, I am able to plot, RMSD between Time (ps) by following command by using GRACE.. g_rms -s md.tpr -f md.xtc xmgrace rmsd.xvg How we can I plot a graph betwwen RMSD and residue no ..?? My aim is to find RMSD at each residues. How i can do that? looking forward for u r important sugg

Re: [gmx-users] RMSD of Aminoacids

Andy Torres wrote: Hi, I'm trying to compare two proteins with the same number of aminoacids with g_confrms, and it works all right, but it gives me the RMSD of the hole protein, and I need the distances (or deviations) of each aminoacid. I know this data shoul be there, but I don't know how to

[gmx-users] RMSD of Aminoacids

Hi, I'm trying to compare two proteins with the same number of aminoacids with g_confrms, and it works all right, but it gives me the RMSD of the hole protein, and I need the distances (or deviations) of each aminoacid. I know this data shoul be there, but I don't know how to get it (I've got the m

Re: [gmx-users] rmsd

shahrbanoo karbalaee wrote: Dear justin I have rmsd graph from peptide (13 amino acid).would you please tell me about generally range of rmsd for good simulation.In my table rmsd start from 2 nm and come up to 3 and change between 3 to 3.5 nm.the solvent is tfe/water.thanks for your advise.

[gmx-users] rmsd

Dear justin I have rmsd graph from peptide (13 amino acid).would you please tell me about generally range of rmsd for good simulation.In my table rmsd start from 2 nm and come up to 3 and change between 3 to 3.5 nm.the solvent is tfe/water.thanks for your advise. best regards -- sh-karbalaee

Re: Re: [gmx-users] rmsd on homologous protein structure

tahnk you i'll try that ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list.

Re: [gmx-users] rmsd on homologous protein structure

Hi, For individual structures, you can use g_confrms. If you want a trajectory you can download do_multiprot from the user contributions section, and follow the instructions there. Note that multiprot aligns based on the structure only (no sequence information). Ran. Tatsiana Kirys wrote: > Hi,

Re: [gmx-users] rmsd on homologous protein structure

Tatsiana Kirys wrote: Hi, i want to calculate rmsd on homologous protein structures that have different residue numbers. As far as i understood g_rms gives only rmsd of the same structure in different configurations, but it doesn't fit homologous protein structures? Yep. In Option -f2 can

[gmx-users] rmsd on homologous protein structure

Hi, i want to calculate rmsd on homologous protein structures that have different residue numbers. As far as i understood g_rms gives only rmsd of the same structure in different configurations, but it doesn't fit homologous protein structures? In Option -f2 can i provide a trajectory of a ho

Re: [gmx-users] rmsd calculation of helix only

ravi sharma wrote: Hello everyone is there any idea how can i calculate rmsd for a given helix or all helix in a protein from a trejectory??? Create an index group, specifying only the residues you care to analyze, and pass it to g_rms. -Justin -Ravi Ravi Datta Sharma Lecturer, Bi

[gmx-users] rmsd calculation of helix only

Hello everyone is there any idea how can i calculate rmsd for a given helix or all helix in a protein from a trejectory??? -Ravi Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut   Send fr

[gmx-users] RMSD

Hi users, I have run two systems of protein simulation for 7ns, the difference between these systems change in the few resdues. After that I have done RMSD analysis. When I superimposed these two 7ns protein simulation systems with crystal structure seperately,I noticed that in one system

Re: [gmx-users] RMSD between

On Sat, 9 Aug 2008, jayant james wrote: hi ! I am interested in plotting the RMSD between two amino acids to see if they come close or move away during simulations. Any suggestions would be helpful. g_mindist Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0

[gmx-users] RMSD between

hi ! I am interested in plotting the RMSD between two amino acids to see if they come close or move away during simulations. Any suggestions would be helpful. Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___

Re: [gmx-users] RMSD, two simulations

On Thu, 26 Jun 2008 13:38:30 +0200 Michal Kolinski <[EMAIL PROTECTED]> wrote: Dear Users, The closest tool to your need is g_rms using the option -m, which generates a matrix of rmsd between all pairs of conformations present in the trajectory. To compare the two trajectories you should concat

Re: [gmx-users] RMSD, two simulations

Hi Michael, g_rms should do the trick. First create an index file having an atom group identical in both systems. Then, g_rms -s ref.pdb -f1 trj1.xtc -f2 trj2.xtc -m rmsd.xpm gives you an rmsd matrix with entry ij given by RMSD[(frame i of trj1),(frame j oftrj2)]. The diagonal of that matrix shoul

[gmx-users] RMSD, two simulations

Dear Users, I've created two different models of the same transmembrane protein. These two models were created using homology approach using two different templates (both with similar sequence similarity to the sequence of the target protein). Next, I did two separate 25ns simulations of th

Re: [Bulk] [gmx-users] RMSD graph

Like Yang Ye said, molecule is likely out of the box (just fix PBC). This also happens when you don't know how to continue a broken simulation (check the WIKI on gmx website) I had this PBC issue many times. What works over here to make things easier is: Be sure that in the reference frame "-s" th

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