Re: [gmx-users] Normal Mode Analysis -- Expected Output

My problem was here: nsteps = 10 which should read nsteps = 1 I was under the assumption that the step numbers would correspond to the number of calculated eigenvectors. All eigenvectors are calculated in step 1. Thanks, Bryan On Thu, Apr 11, 2013 at 12:33 PM, David van der Spoel

[gmx-users] Normal Mode Analysis -- Expected Output

Hello, I am running a normal mode analysis on a ~1500AA protein with the following mdp parameters: Log file opened on Tue Apr 9 09:55:00 2013 Host: uv1 pid: 128985 nodeid: 0 nnodes: 64 Gromacs version:VERSION 4.6.1 Precision: double Memory model: 64 bit MPI library:

Re: [gmx-users] Normal Mode Analysis -- Expected Output

On 2013-04-11 17:57, Bryan Roessler wrote: Hello, I am running a normal mode analysis on a ~1500AA protein with the following mdp parameters: Log file opened on Tue Apr 9 09:55:00 2013 Host: uv1 pid: 128985 nodeid: 0 nnodes: 64 Gromacs version:VERSION 4.6.1 Precision: double

[gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges

Dear GROMACS users, I have done Normal Mode Analysis and have calculated partial charges and the optimized geometry of a few compounds using high-level QM calculations. Now I want to see (if possible) how well GROMACS can reproduce the normal modes if I start from the same optimized geometry and

Re: [gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges

On 20/12/11, Thomas Evangelidis teva...@gmail.com wrote: Dear GROMACS users, I have done Normal Mode Analysis and have calculated partial charges and the optimized geometry of a few compounds using high-level QM calculations. Now I want to see (if possible) how well GROMACS can

Re: [gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges

Mark, thanks for the prompt response! I have done Normal Mode Analysis and have calculated partial charges and the optimized geometry of a few compounds using high-level QM calculations. Now I want to see (if possible) how well GROMACS can reproduce the normal modes if I start from the same

Re: [gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges

On 12/21/2011 12:57 AM, Thomas Evangelidis wrote: Mark, thanks for the prompt response! I have done Normal Mode Analysis and have calculated partial charges and the optimized geometry of a few compounds using high-level QM calculations. Now I want to see (if possible) how well

Re: [gmx-users] Normal Mode Analysis

Hi James, PCA on a trajectory is about fluctuations -the correlation between deviations from an average positions-, NMA is about penalized displacement -the increase in potential energy due to concurrent displacement-. In NMA the lowest mode is that for which most atoms can move most

Re: [gmx-users] Normal Mode Analysis

I've another question about NMA. 1- As I understood the Sparce matrix method is used on default in case when my reference structure consist of alot of atoms. If this true the output Hessian.mtx would be in sparce format, wouldn't it ? 2- How I can convert output.mtx to the txt format ? As the

Re: [gmx-users] Normal Mode Analysis

On 10/11/2011 6:48 AM, James Starlight wrote: I've another question about NMA. 1- As I understood the Sparce matrix method is used on default in case when my reference structure consist of alot of atoms. If this true the output Hessian.mtx would be in sparce format, wouldn't it ? 2- How I

Re: [gmx-users] Normal Mode Analysis

Thank you, Mark. By the way, also I have some question about data analysing From g_anaeig I can obtain atom fluctuations along defined mode 1- Can I obtain same fluctuations along ensemble of several modes (i.e averaged fluctuations along modes from n to k ) in one graph ? 2- Is there any

Re: [gmx-users] Normal Mode Analysis

On 10/11/2011 5:36 PM, James Starlight wrote: Thank you, Mark. By the way, also I have some question about data analysing From g_anaeig I can obtain atom fluctuations along defined mode 1- Can I obtain same fluctuations along ensemble of several modes (i.e averaged fluctuations along

Re: [gmx-users] Normal Mode Analysis

Mark hello, 2011/11/10 Mark Abraham mark.abra...@anu.edu.au From your description, I think you're comparing apples with oranges. I just want compare results of coarse grained NMA based on C-alpha only with full atomic NMA. I've already done that work and obtain that 1- overal picture of

Re: [gmx-users] Normal Mode Analysis

Hi James, 1- Can I obtain same fluctuations along ensemble of several modes (i.e averaged fluctuations along modes from n to k ) in one graph ? The total fluctuation is the sum of the fluctuations along all the modes. To get what you want, you just need to some the fluctuations. Alternatively,

Re: [gmx-users] Normal Mode Analysis

Hi Tsjerk, Thanks for help. So as I understood if I want to calculate fluctuations only for Calpha I must first to do NMA of my reference in some mode subspace consisted of the eigenvectors for Calpha atoms only. Does this correct ? Previously I've done something like this for random subspace of

Re: [gmx-users] Normal Mode Analysis

Mark, hello! I think that there is some error durins saving of my minimization data As the result of the minimization I've obtained (1) Low-Memory BFGS Minimizer converged to machine precision in 3723 steps, but did not reach the requested Fmax 0. Potential Energy = 2.08789280994511e+03

Re: [gmx-users] Normal Mode Analysis

James Starlight wrote: Mark, hello! I think that there is some error durins saving of my minimization data As the result of the minimization I've obtained (1) Low-Memory BFGS Minimizer converged to machine precision in 3723 steps, but did not reach the requested Fmax 0. Potential Energy =

Re: [gmx-users] Normal Mode Analysis

That's energy ouptut from minimization with that parametries ( there is also 1 step of steep minimization before that ) integrator= l-bfgs emtol= 0.001 emstep = 0.001 ; Energy step size nsteps= 50 ; Maximum number of (minimization) steps to perform

Re: [gmx-users] Normal Mode Analysis

On 28/10/2011 2:30 AM, James Starlight wrote: That's energy ouptut from minimization with that parametries ( there is also 1 step of steep minimization before that ) integrator= l-bfgs emtol= 0.001 emstep = 0.001 ; Energy step size nsteps= 50 ;

Re: [gmx-users] Normal Mode Analysis

I've found that in general ussage of cutt-offs beetwen 0.8-1.2 nm might provide good results. But now I have some problems with minimization of my initial structure Firstly, I've performed steep minimization ( emtool=1000, emstep = 0.01 ) and than CG minimization (emtool=1, emstep =

Re: [gmx-users] Normal Mode Analysis

On 26/10/2011 7:54 PM, James Starlight wrote: I've found that in general ussage of cutt-offs beetwen 0.8-1.2 nm might provide good results. But now I have some problems with minimization of my initial structure Firstly, I've performed steep minimization ( emtool=1000, emstep = 0.01 )

Re: [gmx-users] Normal Mode Analysis

Mark hello, 2011/10/26 Mark Abraham mark.abra...@anu.edu.au We don't know the sense in which it didn't minimize properly, so there's not much point us guessing. The output value for Epot was -2.0 after steep minimization and -2.5 after CG. Also as the consequense after both energy

Re: [gmx-users] Normal Mode Analysis

On 26/10/2011 11:04 PM, James Starlight wrote: Mark hello, 2011/10/26 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au We don't know the sense in which it didn't minimize properly, so there's not much point us guessing. The output value for Epot was -2.0 after

Re: [gmx-users] Normal Mode Analysis

Mark, 2011/10/26 Mark Abraham mark.abra...@anu.edu.au Or that your starting structure is not close enough to a sensible minimum for a local gradient-based optimizer to do the job. Look at the atoms with the large forces and see what you can learn. So for that purpose I've done steep

Re: [gmx-users] Normal Mode Analysis

James Starlight wrote: Mark, 2011/10/26 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au Or that your starting structure is not close enough to a sensible minimum for a local gradient-based optimizer to do the job. Look at the atoms with the large forces and

Re: [gmx-users] Normal Mode Analysis

Hi James, Regarding PCA and NMA congruency, they are different things, unless the energy landscape consists of a single harmonic potential well. The principal components and the normal modes will usually correlate quite well, but if the simulation is sampling different energy minima, there may be

Re: [gmx-users] Normal Mode Analysis

Justin, I've forced with the problem that I could not prorerly minimized my system in the NMA conditions. Even in STEEP minimizaation I could not obtain Epot value lower than +3.00 with that parametries ( I've used KALP peptide as a test input ) ; Parameters describing what to do, when to stop

Re: [gmx-users] Normal Mode Analysis

James Starlight wrote: Justin, I've forced with the problem that I could not prorerly minimized my system in the NMA conditions. Even in STEEP minimizaation I could not obtain Epot value lower than +3.00 with that parametries ( I've used KALP peptide as a test input ) The Epot value

Re: [gmx-users] Normal Mode Analysis

I've used double precision. Today I'll copied output because it's done on lab comp but from the output log I've found that minimization was not completed ( e.g when I've calculate Normal Modes with that minimized structure I've obtain message that my system was not minimized properly ) 2011/10/26

Re: [gmx-users] Normal Mode Analysis

As the consequence I've done my NMA calculations without of any constraints :) integrator= nm; Normal Mode Analysis constraints = none but I'm not sure if this could be valid because I didnt found any literature of such NMA in Gromacs. Could someone provide me with the

Re: [gmx-users] Normal Mode Analysis

On 24/10/2011 3:12 AM, James Starlight wrote: I want to come back to the question of the NMA in the Gromacs :) I've found in manual possible algorithms of this analysis- I must calculate Hessian matrix via Md-run and then calculate modes with g_nmens program 1- I've performed CG

Re: [gmx-users] Normal Mode Analysis

On 24/10/2011 6:56 PM, James Starlight wrote: As the consequence I've done my NMA calculations without of any constraints :) integrator= nm; Normal Mode Analysis constraints = none but I'm not sure if this could be valid because I didnt found any literature of such NMA

Re: [gmx-users] Normal Mode Analysis

I understand this but I've not been able found such information. I dont need in the most accurately parametries for all cutt-offs of my system but I want to gain inside into the basic cutt- offs worked with the Normal mode analysis. E.g I've found that PME is not worked here. So I must to

Re: [gmx-users] Normal Mode Analysis

On 25/10/2011 3:30 AM, James Starlight wrote: I understand this but I've not been able found such information. I dont need in the most accurately parametries for all cutt-offs of my system but I want to gain inside into the basic cutt- offs worked with the Normal mode analysis. The cut-offs

Re: [gmx-users] Normal Mode Analysis

I want to come back to the question of the NMA in the Gromacs :) I've found in manual possible algorithms of this analysis- I must calculate Hessian matrix via Md-run and then calculate modes with g_nmens program 1- I've performed CG minimization of my initianl structure 2- I've loadet to the

Re: [gmx-users] Normal Mode Analysis

Thanks It's works fine but I'venot find significant increasing in the simulation speed :) but I'd also to test MPI. Could you tell me what exactly ( MPI or threading) might provide better productivity in case of big heterogenious system ( e.g protein in membrane )? James 2011/10/15 lina

Re: [gmx-users] Normal Mode Analysis

On 16/10/2011 4:31 AM, James Starlight wrote: Thanks It's works fine but I'venot find significant increasing in the simulation speed :) If you've configured with threads, then executing mdrun will spawn as many threads as you have physical cores. This will speed up the calculation so long

[gmx-users] Normal Mode Analysis

Dear Gromacs users! I have couple of questions about some Gromacs features. 1- I'm looking for tutorial where I could find clear example of force fied based Normal Mode Analysis via Gromacs E.g on first step I would like to prepare structure of my protein in pereodic boundary conditions and

Re: [gmx-users] Normal Mode Analysis

On Sat, Oct 15, 2011 at 2:58 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! I have couple of questions about some Gromacs features. 1- I'm looking for tutorial where I could find clear example of  force fied based Normal Mode Analysis via Gromacs E.g on first step I

[gmx-users] Normal Mode Analysis

Hi ALL, This may sound like a very basic question, but I am still pondering over it. I have simulated a membrane protein system for 30 ns after Steepest Descent minimization and now I want to perform NMA. From the help pages what I understand is that I need a very well minimized system (using

[gmx-users] Normal Mode Analysis

Hi ALL, This may sound like a very basic question, but I am still pondering over it. I have simulated a membrane protein system for 30 ns after Steepest Descent minimization and now I want to perform NMA. From the help pages what I understand is that I need a very well minimized system (using

Re: [gmx-users] Normal Mode Analysis

Hi, NMA is not MD - for one thing you don't run an NMA simulation for a certain time. I suggest you read about NMA and make sure you understand what the method does and what it can achieve before continuing. There is some data on the manual, a lot of data on the web and even more in books. When

Re: [gmx-users] Normal Mode analysis

Ajit Datta wrote: Hello everyone, I am trying to do normal mode analysis for a protein using Gromacs. Can anyone point me out towards a sample mdp file that I could edit for this purpose? There are some general pointers here:

Re: [gmx-users] Normal Mode analysis

Aside from that, search the literature; published papers should have reproducible methodology :) And.., methodology in published papers has proven to be publishable. :) Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing

[gmx-users] Normal Mode analysis

Hello everyone, I am trying to do normal mode analysis for a protein using Gromacs. Can anyone point me out towards a sample mdp file that I could edit for this purpose? Thanks Ajit B. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] normal mode analysis

Hi Gromacs User's, In the normal mode analysis if I get the first 6 eigenfrequency zero then I can think that the the protein is properly energy minimized. Thank you Abhijit ___ gmx-users

[gmx-users] Normal mode analysis of pure water

Hi, I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution. mdrun_d -v -s water.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log -mtx nm.mtx Getting Loaded... Reading file water.tpr, VERSION 4.0.4 (double precision) Loaded with

Re: [gmx-users] Normal mode analysis of pure water

simon sangma wrote: Hi, I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution. You've been told twice already what the likely solution is: snip Maximum force: 2.74758e+03 Maximum force probably not small enough to ensure

[gmx-users] Normal mode analysis of pure water

Hi Justin, I tried altering the .mdp file (integrator = steep instead of nm) for energy minimization. But in that case the mdrun did not generate the Hessian matrix (nm.mtx) inspite of using the command twice. ___ gmx-users

Re: [gmx-users] Normal mode analysis of pure water

simon sangma wrote: Hi Justin, I tried altering the .mdp file (integrator = steep instead of nm) for energy minimization. But in that case the mdrun did not generate the Hessian matrix (nm.mtx) inspite of using the command twice. Energy minimization is not the

RE: [gmx-users] Normal mode analysis of pure water

:43 +0530 From: simoniitc...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Normal mode analysis of pure water Hi, I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution. mdrun_d -v -s water.tpr -o traj.trr -c confout.gro

[gmx-users] Normal mode analysis of pure water

Hi Berk, You mentioned that standard NMA techniques will not work for the liquid water system. Could you suggest the alternatives then? ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

RE: [gmx-users] Normal mode analysis of pure water

2009 19:20:19 +0530 From: simoniitc...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Normal mode analysis of pure water Hi Berk, You mentioned that standard NMA techniques will not work for the liquid water system. Could you suggest the alternatives

[gmx-users] Normal mode analysis of pure water

Hi Justin, Are you suggesting that after thorough energy minimization, seperate .mdp file is to be used for NMA? In that case how would that output file (energy minimised file) be taken as an input file for the grompp and mdrun command (for NMA)? What extension would the file have

Re: [gmx-users] Normal mode analysis of pure water

simon sangma wrote: Hi Justin, Are you suggesting that after thorough energy minimization, seperate .mdp file is to be used for NMA? In that case how would that output file (energy minimised file) be taken as an input file for the grompp and mdrun command (for NMA)? What

[gmx-users] Normal mode analysis

Hi, If I going to perform normal mode analysis of a protien molecule what are the changes have to be done in .mdp files Abhijit Kayal IIT Delhi

Re: [gmx-users] Normal mode analysis

abhijit kayal wrote: Hi, If I going to perform normal mode analysis of a protien molecule what are the changes have to be done in .mdp files That's what the manual is for, as well as pertinent literature and textbooks describing the protocols. -Justin Abhijit Kayal

[gmx-users] Normal mode analysis

Hi! I am a user of gromacs. Could someone provide me with a method (or set of commands) for normal mode analysis of small molecules (water, n-butane, etc). Also could you please provide a command for generating Hessian Matrix after the energy minimization.

Re: [gmx-users] Normal mode analysis

simon sangma wrote: Hi! I am a user of gromacs. Could someone provide me with a method (or set of commands) for normal mode analysis of small molecules (water, n-butane, etc). Also could you please provide a command for generating Hessian Matrix after the energy minimization. You should

Re: [gmx-users] Normal Mode Analysis

, if required. Berk -- Date: Tue, 26 May 2009 14:47:52 +0200 Subject: Re: [gmx-users] Normal Mode Analysis From: f.hoffga...@gmail.com To: gmx-users@gromacs.org Hi thanks for your reply. I tried patching as you described it, but I got the error message: patch

[gmx-users] Normal Mode Analysis

Hi, I'm quite a new user of gromacs. I want to do an all-atom normal mode analysis of a small protein in water. As a result I would like to have the hessian matrix in a readable format, that I can use for further computations. As I have read in the manuals/tutorials/mailing-lists I minimized the

RE: [gmx-users] Normal Mode Analysis

Hi, Try renaming it with the extension .trr iso .trj. Berk Date: Tue, 26 May 2009 10:53:32 +0200 From: f.hoffga...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Normal Mode Analysis Hi, I'm quite a new user of gromacs. I want to do an all-atom normal mode analysis of a small

Re: [gmx-users] Normal Mode Analysis

. Berk -- Date: Tue, 26 May 2009 10:53:32 +0200 From: f.hoffga...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Normal Mode Analysis Hi, I'm quite a new user of gromacs. I want to do an all-atom normal mode analysis of a small protein in water

RE: [gmx-users] Normal Mode Analysis

Hi, I just saw that 4.0 uses a new mtx format which can also efficiently store sparse matrices. Please try if my modified gmxdump for 4.0.5 works? Store the data below in a file called fix and then do: patch gmxdump.c fix Berk 61a62,63 #include

Re: [gmx-users] Normal Mode Analysis

Hi thanks for your reply. I tried patching as you described it, but I got the error message: patch: `' expected at line 18 of patch Franzi --- Franziska Hoffgaard PhD Student Bioinformatics Theo. Biology Group TU Darmstadt 2009/5/26 Berk Hess g...@hotmail.com Hi, I just saw that

RE: [gmx-users] Normal Mode Analysis

-users] Normal Mode Analysis From: f.hoffga...@gmail.com To: gmx-users@gromacs.org Hi thanks for your reply. I tried patching as you described it, but I got the error message: patch: `' expected at line 18 of patch Franzi --- Franziska Hoffgaard PhD Student Bioinformatics Theo. Biology

[gmx-users] Normal mode analysis

Hi All, I am doing normal mode analysis. After getting the eigen frequencies, is there a way we can visualize the vibrational modes in gromacs. And even how to know which frequency corresponds to which mode of vibration. I saw that IED is used to visualize normal modes by integrating

Re: [gmx-users] Normal Mode Analysis in Double-Precision

Inon Sharony wrote: This is exactly the point - I get only three significant digits. Although I performed the entire procedure in double-precision. The convergence to 5E-4 DID occur in single-precision, I just thought it wasn't good enough (the program recommends 1E-5 and when

Re: [gmx-users] Normal Mode Analysis in Double-Precision

Dear Ran, I'm still unsure of why I sometimes can get double-precision output and sometimes not. I can't find what I'm doing differently in each case, however I now know what to look for in order to be sure that I'm getting what I need. Obviously, the need for double-precision stems only

Re: [gmx-users] Normal Mode Analysis in Double-Precision

This is exactly the point - I get only three significant digits. Although I performed the entire procedure in double-precision. The convergence to 5E-4 DID occur in single-precision, I just thought it wasn't good enough (the program recommends 1E-5 and when double-precision works for me I

Re: [gmx-users] Normal Mode Analysis in Double-Precision

Inon Sharony wrote: Dear Ran, I'm still unsure of why I sometimes can get double-precision output and sometimes not. I can't find what I'm doing differently in each case, however I now know what to look for in order to be sure that I'm getting what I need. Obviously, the need for

Re: [gmx-users] Normal Mode Analysis in Double-Precision

Quoting Ran Friedman [EMAIL PROTECTED]: Inon Sharony wrote: Dear Ran, I'm still unsure of why I sometimes can get double-precision output and sometimes not. I can't find what I'm doing differently in each case, however I now know what to look for in order to be sure that I'm getting what

Re: [gmx-users] Normal Mode Analysis in Double-Precision

How do I get a *.gro file in double-precision, then? The configurations given by the PRODRG server are in 0.000 format, and still I've at least once managed to get double-precision calculations out of them (right now I'm working on a file for a Pentane molecule, originally downloaded from

Re: [gmx-users] Normal Mode Analysis in Double-Precision

The *.gro file always has 3 significant digits, but the *.tpr file sometimes has the coordinates with 5 significant digits and sometimes the last two of those are zero. Quoting Ran Friedman [EMAIL PROTECTED]: How do I get a *.gro file in double-precision, then? The configurations given

Re: [gmx-users] Normal Mode Analysis in Double-Precision

You can also try: gmxdump -f em.trr | grep precision Inon Sharony wrote: The *.gro file always has 3 significant digits, but the *.tpr file sometimes has the coordinates with 5 significant digits and sometimes the last two of those are zero. Quoting Ran Friedman [EMAIL PROTECTED]: How

Re: [gmx-users] Normal Mode Analysis in Double-Precision

I now performed: make distclean ./configure --disable-float make make install make links All executed without problems. Now I no longer have segmentation faults (thanks David!), however the energy minimization still does not achieve 1E-05 kJ / mole nm convergence (only as good as ~5E-04

[gmx-users] Normal Mode Analysis in Double-Precision

Hi all! I'm trying to perform a normal mode (NM) analysis, but having trouble with the recommendation of first performing a double precision energy minimization before writing the Hessian. The calculation of the Hessian matrix is done using mdrun, and its diagonalization is done using

Re: [gmx-users] Normal Mode Analysis in Double-Precision

Hi, It's hard to know why you get a segmentation fault without further info. Did you ran the GMX tests after installation with double precision? Is everything all right there? Also, when exactly the system crashes? Is it straight when you start mdrun? Did you use both grompp and mdrun in double

Re: [gmx-users] Normal Mode Analysis in Double-Precision

Hi Ran. I looked up your suggestions, and got the following: 0. The parameters in the *.tpr file appear in 0.e+00 format. How can I tell if this is a float or double? Also, I could not see if the position coordinates of the molecule appear in the *.tpr file (and if so, if they

Re: [gmx-users] Normal Mode Analysis in Double-Precision

Inon Sharony wrote: Hi Ran. I looked up your suggestions, and got the following: 0. The parameters in the *.tpr file appear in 0.e+00 format. How can I tell if this is a float or double? Also, I could not see if the position coordinates of the molecule appear in the *.tpr file

Re: [gmx-users] Normal Mode Analysis in Double-Precision

Ran Friedman wrote: Inon Sharony wrote: Hi Ran. I looked up your suggestions, and got the following: 0. The parameters in the *.tpr file appear in 0.e+00 format. How can I tell if this is a float or double? Also, I could not see if the position coordinates of the molecule

Re: [gmx-users] normal mode analysis

Hi, On Friday, 21. December 2007 12:48, Robert Fenwick wrote: Hi, I am interested in comparing the normal modes of a protein with and without a ligand. I have already computed the lowest 100 normal modes for the protein (eigenvec_a.trr) and the protein:ligand complex and have reduced the

Re: [gmx-users] normal mode analysis

Robert Fenwick wrote: Hi, I am interested in comparing the normal modes of a protein with and without a ligand. I have already computed the lowest 100 normal modes for the protein (eigenvec_a.trr) and the protein:ligand complex and have reduced the protein:ligand eigenvec_b.trr to the

[gmx-users] normal mode analysis

Hi, I am interested in comparing the normal modes of a protein with and without a ligand. I have already computed the lowest 100 normal modes for the protein (eigenvec_a.trr) and the protein:ligand complex and have reduced the protein:ligand eigenvec_b.trr to the protein by issuing;

Re: [gmx-users] Normal Mode Analysis

Hi, First, it's just a warning that the force _might_ not be small enough since there's no bullet-proof way to say. In general, both for final-stage energy minimization (with L-BFGS) and actual normal mode analysis you can use a setup with double precision switched coulomb vdw

[gmx-users] normal mode analysis (size issue)

Hi, I want to carry out normal mode analysis on a large protein (about 10,000 atoms) without using coarse grain approximations. Amber is out of the question since it can only handle about 5,000 atoms for NMA. I am wondering if GROMACS can deal with this assuming running on a 64-bit machine with

Re: [gmx-users] normal mode analysis (size issue)

Hi, On Jun 19, 2007, at 5:26 PM, Liwei Li wrote: I want to carry out normal mode analysis on a large protein (about 10,000 atoms) without using coarse grain approximations. Amber is out of the question since it can only handle about 5,000 atoms for NMA. I am wondering if GROMACS can deal

[gmx-users] Normal mode analysis - reference [34] in the Gromacs manual

It seems like reference #34 in the GMX 3.3 manual should be: Levitt, M., Sander, C. and Stern PS. The normal modes of a protein: native bovine pancreatic trypsin inhibitor. Internatl. J. Quant.Chem., Quantum Biology Symposium 10, 181-199. 1983 And not as written. Ran. --

Re: [gmx-users] Normal mode analysis - reference [34] in the Gromacs manual

Ran Friedman wrote: It seems like reference #34 in the GMX 3.3 manual should be: Levitt, M., Sander, C. and Stern PS. The normal modes of a protein: native bovine pancreatic trypsin inhibitor. Internatl. J. Quant.Chem., Quantum Biology Symposium 10, 181-199. 1983 And not as written. Ran.