Re: [gmx-users] g_covar

Hi Karbalee, It says : nanometer squared. Cheers, Tsjerk PS. Many of us are not Justin... :p On Sat, Jan 15, 2011 at 5:33 PM, shahrbanoo karbalaee wrote: > Dear Justin > Hi,I want to use PCA for compare fluctuations two  peptides with  13 > aa. I  use this command g_covar > g_covar #NAME?  ru

Re: [gmx-users] g_covar

- Original Message - From: pawan raghav Date: Wednesday, June 2, 2010 4:18 Subject: [gmx-users] g_covar To: gmx-users@gromacs.org > Thanks Mark for your advice > > Note: The fit analysis group are identical, > while the fit is mass weighted and the analysis is not making the fit non

Re: [gmx-users] g_covar

Hi, Fitting is commonly done mass weighted if the reference file contains masses, like a run input file. But covariance analysis is only performed mass weighted if explicitly requested (and masses are available). If mass-weighted analysis is not requested, the masses for the fit will all be set to

Re: [gmx-users] g_covar

Hi Kavya, Each atom has three coordinates; 3*3740=11220 coordinates, yielding as many eigenvalues and -vectors. Cheers, Tsjerk On Wed, Jun 1, 2011 at 2:44 PM, Kavyashree M wrote: > Dear users, > > I was using g_covar (gmx 4.5.3) to find the eigenvalue and > eigenvectors. When I used f

Re: [gmx-users] g_covar

Thanks Sir, Thanks just now I figured it out! With regards kavya On Wed, Jun 1, 2011 at 6:20 PM, Tsjerk Wassenaar wrote: > Hi Kavya, > > Each atom has three coordinates; 3*3740=11220 coordinates, yielding as > many eigenvalues and -vectors. > > Cheers, > > Tsjerk > > On Wed, Jun 1, 2011 at 2:4

Re: [gmx-users] g_covar

Hi Gideon, > First, is there anyway to specify that the covar.dat output will be in R > distance (meaning sqrt(x^2+y^2+Z^2)) and not in separate Cartesian > coordinates? also when examining the output I don't understand how the main > diagonal values are different than 1, for instance the x1x1 > c

Re: [gmx-users] g_covar

Hi. > Second, Say I would like to analyze the main difference between two > trajectories of the same protein using PCA. is it KOSHER to use the same > first frame which is identical between both runs as the reference strucutre > and then just append both runs into a single trajectory and then use

Re: [gmx-users] g_covar

Hi, > This questuion may be hard. You need rabbi's advice)) > But there are some feature of the reference structure that makes it good or > bad. It is mean deviation of the atomic coordinates of the fited structures > from the reference, the best reference minimizes this measure. For a rigid > str

Re: [gmx-users] g_covar

I know, but the best reference is "mean". And it is another mean that calculated after fit at some frame. 2011/8/16 Tsjerk Wassenaar > Hi, > > > This questuion may be hard. You need rabbi's advice)) > > But there are some feature of the reference structure that makes it good > or > > bad. It is

Re: [gmx-users] g_covar

Hey Yuri, What do you mean with mean? Mean without fitting is a single point. Mean only makes sense after aligning. Now there's a nice recursive problem: 1. Calculate mean to get reference 2. Align to reference to calculate mean (http://xkcd.com/754/) But think about it... aligning to some refere

Re: [gmx-users] g_covar

Hi Tsjerk. What do you mean with mean? Mean without fitting is a single point. > Mean only makes sense after aligning. Now there's a nice recursive > problem: > 1. Calculate mean to get reference > 2. Align to reference to calculate mean I mean the limit of this sequence is mean) Because it is n

Re: [gmx-users] g_covar

Carla Jamous wrote: Hi everyone, please I'm using gromacs 4.0.3, and I want to see the program g_covar, except that I have it in binary file and I want to see the C program in text format. Please how can I have access to it? Download the source code, then look at src/tools/gmx_covar.c.

RE: [gmx-users] g_covar

YourSourceCode/gromacs/src/tools/ If in Linux OS, try locate g_covar.c p.s 4.0.3 is not the latest version. why do not try the latest version? From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Carla Jamous [carlajam...@gmail.co

Re: [gmx-users] g_covar

tangxuan wrote: Mark Abraham wrote: tangxuan wrote: Thanks for your reply. I have another question. I can get the coordinates covariance by option -ascii, but do you know how to get a exact covariance value for each atom? How do you mean "exact", and in what format? Mark __

Re: [gmx-users] g_covar

Mark Abraham wrote: tangxuan wrote: Mark Abraham wrote: tangxuan wrote: Thanks for your reply. I have another question. I can get the coordinates covariance by option -ascii, but do you know how to get a exact covariance value for each atom? How do you mean "exact", and in what format? Ma

RE: [gmx-users] g_covar

This is an incorrect warning, which has been introduced in version 3.3.2. I have corrected the warning for 3.3.3. Berk. > Date: Wed, 9 Jan 2008 14:51:52 +0100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] g_covar > > Dear all, > When I am using g_covar to calcula

Re: [gmx-users] g_covar

Berk Hess wrote: This is an incorrect warning, which has been introduced in version 3.3.2. I have corrected the warning for 3.3.3. Berk. Date: Wed, 9 Jan 2008 14:51:52 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] g_covar Dear all, When I am using g_covar to

Re: [gmx-users] g_covar

tangxuan wrote: Thanks for your reply. I have another question. I can get the coordinates covariance by option -ascii, but do you know how to get a exact covariance value for each atom? How do you mean "exact", and in what format? Mark ___ gmx-user

Re: [gmx-users] g_covar

Mark Abraham wrote: tangxuan wrote: Thanks for your reply. I have another question. I can get the coordinates covariance by option -ascii, but do you know how to get a exact covariance value for each atom? How do you mean "exact", and in what format? Mark ___

RE: [gmx-users] g_covar -ascii

Hello, I am interested in dynamical analysis of my protein. In the manual, it says -ascii generates a file that includes the whole covariance matrix, and -xpma writes the atomic covariance matrix per pair of atoms. I was wondering if there is a way to have this atomic covariaces in the .dat file wi

Re: [gmx-users] g_covar -ref

Hi Vijaya, Well, to start with that will be something as calculating the 'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith atom of the conformation x and the reference structure r and the sum is over time/observations. In the case of no variation in xi, the value you get will stil

RE: [gmx-users] g_covar -ref

Thu, 18 Mar 2010 17:51:04 +0100 > Subject: Re: [gmx-users] g_covar -ref > From: tsje...@gmail.com > To: gmx-users@gromacs.org > > Hi Vijaya, > > Well, to start with that will be something as calculating the > 'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoti

Re: [gmx-users] g_covar -ref

by projecting the trajectory onto >  the eigenvectors of the covariance matrix. > I just wanted to know why the option -ref was offered and if it had any > significance. > Thanks > Vijaya > >> Date: Thu, 18 Mar 2010 17:51:04 +0100 >> Subject: Re: [gmx-users] g_covar -

RE: [gmx-users] g_covar -ref

Hi Your answer truly eludes me, unless -ref is an useless option. In any case it isn't particularly important. Vijaya > Date: Thu, 18 Mar 2010 19:37:40 +0100 > Subject: Re: [gmx-users] g_covar -ref > From: tsje...@gmail.com > To: gmx-users@gromacs.org > > Hi Vijaya, >

Re: [gmx-users] g_covar -ref

results then mean? This is a neat example to run with pen and paper... You should even be able to solve it analytically :) Have fun, Tsjerk > In any case it isn't particularly important. > Vijaya > > > >> Date: Thu, 18 Mar 2010 19:37:40 +0100 >> Subject: Re: [gmx-u

RE: [gmx-users] g_covar -ref

Hi Thanks for your input, what are the few specific cases where a reference structure might be used? Vijaya > Date: Thu, 18 Mar 2010 20:42:36 +0100 > Subject: Re: [gmx-users] g_covar -ref > From: tsje...@gmail.com > To: gmx-users@gromacs.org > > Hi Vijaya, > > >

Re: [gmx-users] g_covar -ref

, Tsjerk On Thu, Mar 18, 2010 at 9:11 PM, vijaya subramanian wrote: > Hi > Thanks for your input, what are the few specific cases where > a reference structure might be used? > Vijaya > >> Date: Thu, 18 Mar 2010 20:42:36 +0100 >> Subject: Re: [gmx-users] g_covar -ref >&

Re: [gmx-users] g_covar Segmentation fault

Anirban Ghosh wrote: Hi ALL, I have a system of beads with which I ran a CGMD (coarse grained MD) using NAMD. Now I want to do a PCA analysis of this system using GROMACS. So I converted the trajectory in .trr format and made an index file of the entire system (45 beads). But now when I try t

Re: [gmx-users] g_covar Segmentation fault

Anirban Ghosh a écrit : Hi ALL, I have a system of beads with which I ran a CGMD (coarse grained MD) using NAMD. Now I want to do a PCA analysis of this system using GROMACS. So I converted the trajectory in .trr format Convert a dcd file into a trr file is not that straightforward. How did y

Re: [gmx-users] g_covar & g_anaeig problems

Hi Jared, Can you post the exact series of commands you used to come to this point, including the selections you used and what constitutes these selections if they are not standard? Please also indicate what was in the trajectory you started off with (xtc-grps). Cheers, Tsjerk On Thu, Mar 25, 2

Re: [gmx-users] g_covar : segmentation fault

Poojari, Chetan wrote: Hi, I am doing Dihedral PCA and followed the steps as mentioned in the Gromacs documentation http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA Below are the commands i used: 1) I generated index file for chosen dihedral angles. 2) g_angle -f 100ns_noPBC.xtc

Re: [gmx-users] g_covar & g_anaeig problems

Hey everyone, searching the list for the answer to a g_covar problem I've found this post of Arne who describes the very same problem that I encounter. I'm observing this problem on a linux cluster with 32GB memory on each node. The g_covar_d application was compiled in double precision with

Re: [gmx-users] g_covar & g_anaeig problems

- Original Message - From: Sebastian Breuers Date: Tuesday, September 7, 2010 0:42 Subject: Re: [gmx-users] g_covar & g_anaeig problems To: gmx-users@gromacs.org > Hey everyone, > > searching the list for the answer to a g_covar problem I've > found this post

Re: [gmx-users] g_covar & g_anaeig problems

esday, September 7, 2010 0:42 Subject: Re: [gmx-users] g_covar & g_anaeig problems To: gmx-users@gromacs.org > Hey everyone, > > searching the list for the answer to a g_covar problem I've > found this post of Arne who describes the very same problem that > I encounter. > > I&

Re: [gmx-users] g_covar & g_anaeig problems

- Original Message - From: Sebastian Breuers Date: Tuesday, September 7, 2010 17:47 Subject: Re: [gmx-users] g_covar & g_anaeig problems To: gmx-users@gromacs.org > Hey, > > taking fewer atoms by ignoring the hydrogens is a good advice. > Thanks a lot. That'

Re: [gmx-users] g_covar average.pdb calculation

Hi Deniz, The option -ref/-noref is not what you think it is. You want to use -nofit. Cheers, Tsjerk On Fri, Sep 20, 2013 at 2:26 PM, Deniz Aydin wrote: > Dear All, > > I would like to get information on how g_covar calculates the average > structure file (average.pdb) > > My aim was actuall

Re: [gmx-users] g_covar with individual masses

On 4/15/13 5:17 AM, Sebastian Waltz wrote: Dear Gromacs users, I want to calculate the covariance matrix of the center of mass coordinates of non standard residues. Since I want to do it mass weighted I need to give the center of mass masses. From which file does g_covar read the masses? Th

Re: [gmx-users] g_covar to calculate correlation of motion

Hi Bipin, Try using a .gro or .pdb file as reference structure (-s). Only .tpr files are version specific. Cheers, Tsjerk On Feb 21, 2011 8:05 AM, "bipin singh" wrote: Dear GMX users, I want to calculate the correlated motion between atoms during the md simulation for that purpose I am using

Re: [gmx-users] g_covar to calculate correlation of motion

Hi, Thanks for your suggestion. While running the g_covar it is showing the error that aminoacids.dat is not found, so i have copied the residuetypes.dat(which i seems the new modified name for aminoacids.dat in current GROMACS version), then it prompts to choose the group for least square fit, whi

Re: [gmx-users] g_covar to calculate correlation of motion

Hi Bipin, The file residuetypes.dat is quite different from aminoacids.dat. You can paste the following into that file (first line is number of entries, followed by so many residue names): 49 ABU ACE AIB ALA ARG ARGN ASN ASN1 ASP ASP1 ASPH CYS CYS1 CYS2 CYSH DALA GLN GLU GLUH GLY HIS HIS1 HI

Re: [gmx-users] g_covar to calculate correlation of motion

Thanks a lot Sir. On Mon, Feb 21, 2011 at 15:26, Tsjerk Wassenaar wrote: > Hi Bipin, > > The file residuetypes.dat is quite different from aminoacids.dat. You > can paste the following into that file (first line is number of > entries, followed by so many residue names): > > 49 > ABU > ACE > AIB

Re: [gmx-users] g_covar ends up complaining from a Segmentation Fault

Peyman Yamin wrote: Hello everybody, in an attempt to calculate the free-energy surface of a peptide, i followed exactly the procedure described in >> http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA <<< except that g_angle seems to need no -s option in my gromacs version(4.0.5).