Re: [gmx-users] is there any tool for flexibility?

to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Thomas Evangelidis PhD

[gmx-users] sequentially fitting each frame of one trajectory to each frame of another trajectory

trajectory. Is there any GMX tool that can do that? thanks, Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens

Re: [gmx-users] sequentially fitting each frame of one trajectory to each frame of another trajectory

. Sorry. May I ask how you did the MinVar fitting? Cheers, Tsjerk On Mon, Jun 17, 2013 at 12:55 PM, Thomas Evangelidis teva...@gmail.com wrote: Dear GROMACS list, I used minVar to remove global rotations and translations from a trajectory, but due to memory issues I used a replica

Re: [gmx-users] Dihedral angle PCA

On 12 April 2013 07:51, anu chandra anu80...@gmail.com wrote: Hi David, Thanks for the reply. I have not tried yet. Since I didn’t find query about the dihedral PCA in the mail list, I thought of confirm about the steps mentioned in the web site. Regarding the use of dihedral PCA, the

Re: [gmx-users] Dihedral angle PCA

dPCA is preferred in cases of peptides or intrinsically disordered proteins. And even then a disordered mess can still be a disordered mess... Very true! -- == Thomas Evangelidis PhD student University of Athens

Re: [gmx-users] GPU warnings

gcc 4.7.2 is not supported by any CUDA version. I suggest that you just fix it by editing the include/host_config.h and changing the version check macro (line 82 AFAIK). I've never had real problems with using new and officially not supported gcc-s, the version check is more of a promise

Re: [gmx-users] GPU warnings

Hi Szilárd, I was able to run code compiled with icc 13 on Fedora 17, but as I don't have Intel Compiler v13 on this machine I can't check it now. Please check if it works for you with gcc 4.7.2 (which is the default) and let me know if you succeed. The performance difference between icc and

Re: [gmx-users] GPU warnings

/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Thomas

Re: [gmx-users] GPU warnings

2.15-57.fc17 @updates On Fri, Nov 9, 2012 at 5:51 PM, Thomas Evangelidis teva...@gmail.comwrote: I get these two warnings when I run the dhfr/GPU/dhfr-solv-PME.bench benchmark with the following command line: mdrun_intel_cuda5 -v -s topol.tpr -testverlet

Re: [gmx-users] GPU warnings

-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli

Re: [gmx-users] GPU warnings

/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev

Re: [gmx-users] criterion of the convergence of the simulation

-- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site

Re: [gmx-users] about salt concentration

revisited: extensive molecular dynamics simulations and analysis of protein structures in alkali-chloride solutions}, journal = J Phys Chem B, year = 2011, volume = 115, pages = 9213-9223 } Ran Message: 6 Date: Thu, 11 Oct 2012 23:41:11 +0300 From: Thomas Evangelidis teva...@gmail.com

Re: [gmx-users] about salt concentration

-- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https

Re: [gmx-users] Interaction study for peptide-receptor..

the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department

Re: [gmx-users] pca-based MD

. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department

Re: [gmx-users] pca-based MD

site) is affected from the 1st PC by 70%, from the 2nd by 5%, from the 3rd by 12%, and from the 4th by 7% and to the 5th by 6%. It is more accurate then to use PC1-5 in ED sampling. 2012/9/23 Thomas Evangelidis teva...@gmail.com: I presume you are referring to Essential Dynamics Sampling

Re: [gmx-users] PCA comparison between two simulations

to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy

Re: [gmx-users] pca-based MD

. Unfortunately they are not implemented in GROMACS, but they are in AMBER. Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71

[gmx-users] laptop GPU support

Dear GROMACS community, I am about to buy a new laptop so I would like to know if GROMACS supports, or will support in the future, any of the following GPUs: NVIDIA GeForce GT 630M, 640M or 650M Thank you in advance, Thomas -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] some hardware questions

/Mailing_Lists -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https

[gmx-users] minimum distance between periodic images does not aggree with box dimensions

in advance. Thomas -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https

Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron

and the longest diameter is pretty small. That means that there isn't really an optimal orientation in a rhombic dodecahedron; all orientations are pretty much equal. And that's how it should be :) Cheers, Tsjerk On Thu, Apr 26, 2012 at 1:18 PM, Thomas Evangelidis teva...@gmail.com wrote: Dear

Re: [gmx-users] Re: questions about Principal Component Analysis

-- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site

Re: [gmx-users] Re: questions about Principal Component Analysis

-- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- gmx

Re: [gmx-users] Principal Components Analysis in Gromacs

PCA on both sets separately and then g_anaeig -v eigenvec_from_md.trr -v2 eigenvec_from_xray.trr -eig eigenval_from_md.xvg -eig2 eigenval_from_xray.xvg -s reference.tpr -inpr -- == Thomas Evangelidis PhD student

[gmx-users] cluster analysis of flexible peptide trajectory

Dear GROMACS users, Obviously RMSD-based clustering is not the best approach to find frequently visited conformations of flexible peptides. The other approach would be to used backbone dihedral angles to cluster the frames (i.e. with g_dih). There are also several articles in the literature

[gmx-users] Re: questions about Principal Component Analysis

would GREATLY appreciate any comments!!! Thomas On 7 March 2012 21:56, Thomas Evangelidis teva...@gmail.com wrote: Dear GROMACS community, I have two questions regarding PCA. I have run MD simulations for 70 ns for a protein of 1100 amino acids, of which I decided - based on the RMSD

[gmx-users] questions about Principal Component Analysis

. Is it right to do draw conclusion from PCA restricted that domain (400 aa)? 2) How can I find out if the simulation time is sufficient to do PCA? Thanks in advance for any feedback. Thomas -- == Thomas Evangelidis PhD student

Re: [gmx-users] md in vacuo

On 29 February 2012 14:04, Mark Abraham mark.abra...@anu.edu.au wrote: On 29/02/2012 8:33 PM, Thomas Evangelidis wrote: Dear GROMACS community, I use the following parameters to run MD of ethane in vacuo. Then I calculate the H-C-C-H dihedral angle distribution and from

[gmx-users] rules of thumb to select a cutoff for clustering

appreciate any advice! Thomas -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com

Re: [gmx-users] Protein Structure Prediction

and of course I am not an expert in this field. I do not want to open a huge discussion with personal attacks as it is usually done in this list. Bests, Emanuel -- == Thomas Evangelidis PhD student Biomedical Research Foundation

Re: [gmx-users] Protein Structure Prediction

terminal) is 150. They have similar sequence as they are polyglycine peptides which are known to form loops (beta loops). Steven On Mon, Jan 9, 2012 at 9:52 AM, Thomas Evangelidis teva...@gmail.comwrote: Hi, The problem with I-TASSER is that you cannot use the desired templates for threading

[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

? grompp_d4.5.5 -f nm.mdp -c ${ligand}_8_decimal_points.gro -p ${ligand}.top -o nm.tpr Thomas == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens

Re: [gmx-users] amber99sb in GROMACS vs amber99sb in AMBER

-- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage

[gmx-users] amber99sb in GROMACS vs amber99sb in AMBER

. Differences in speed would be also interesting but of secondary importance. thanks in advance. Thomas -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27

[gmx-users] Re: cannot inactivate fitting in g_rmsf - incomplete coordinates are written

Surprisingly I could get complete coordinates from g_covar v4.5.4 without fitting, without being prompted to choose a group for the least squares fit. However, g_covar is much slower than g_rmsf and I would avoid using it for the whole trajectory if I could. I don't expect o get an answer in

[gmx-users] cannot inactivate fitting in g_rmsf - incomplete coordinates are written

Dear GROMACS community, I am trying to calculate B-factors of a sample equilibrated system (31 frames). My trajectory is in .psf and .dcd format but I have created a .tpr file for my analysis from the first frame . First I eliminated random translation and rotation of my protein by fitting every

Re: [gmx-users] Single long simulation versus multiple short

interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou

[gmx-users] NMR chemical shift restraints

restraints with a given propensity) during MD simulations. I would be grateful if any experienced member could clarify this for me. thanks in advance, Thomas -- == Thomas Evangelidis PhD student Biomedical Research Foundation

Re: [gmx-users] oplsaa vs. charmm

such? I'd imagine that IDP simulations with either forcefield would only be qualitatively accurate given that the forcefields are calibrated, as you say, on rigid proteins and small molecules. On 6/8/11 8:00 AM, Thomas Evangelidis wrote: Dear Prof van der Spoel and GROMACS users

Re: [gmx-users] oplsaa vs. charmm

to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy

Re: [gmx-users] flexibility

to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy

Re: [gmx-users] about side chain and structure rifinement

)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Thomas Evangelidis PhD student Biomedical Research Foundation

Re: [gmx-users] about side chain and structure rifinement

the results if you're interested on it. cheer marco On 17 May 2011 12:20, Thomas Evangelidis teva...@gmail.com wrote: A MM ff like OPLS will probably do your job. However CASP experiments show that knowledge-based potentials like the one Rosetta implements, produce more physically realistic

Re: [gmx-users] Adding water to protein to start the simulation process

-- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- gmx-users mailing

Re: [gmx-users] Re : Simulation for prediction of binding between a peptide and protein

, Thomas Evangelidis teva...@gmail.comwrote: You can try Rosetta for flexible peptide docking. On 11 April 2011 15:32, Mark Abraham mark.abra...@anu.edu.au wrote: Hi, I want to know how can I predict where a designed peptide will bind to my protein target or not using simulation ... Can

Re: [gmx-users] Re : Simulation for prediction of binding between a peptide and protein

://www.gromacs.org/Support/Mailing_Lists -- == Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tev...@bioacademy.gr teva...@gmail.com

Re: [gmx-users] Minimisation restraints

don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Thomas Evangelidis PhD student

Re: [gmx-users] percentage of secondary structure

This is the way to do it with Pymol for one frame: http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg08154.html I guess with a little bit of python scripting you could read through all the frames of your trajectory. Thomas 2011/1/4 ahmet yıldırım ahmedo...@gmail.com I get the

Re: [gmx-users] How to force gromacs to fix all bad bonds and angles in a homology model?

This is a bit off-topic but if you want to improve dihedral angles, bond angles and distances, rotamers along with steric clashes, IMO PyRosetta is more efficient than GROMACS. I use ClassicRelax protocol with the 'standard' score function in conjunction with the 'score12' patch ('score12' patch

Re: [gmx-users] protein folding

With respect to protein folding, I want to fold a 42 amino acid loop (part of a protein domain with known structure) which has no homologous counterpart in PDB. Ab initio servers fail to assign a compact tertiary structure to the loop, so I would like to see how MD tools can cope with this

[gmx-users] Energy minimization: problems with ramachanrad score

I 'm trying to relax my homology models from steric clashes, and while searching for the appropriate minimization scheme, I came across this old thread: http://lists.gromacs.org/pipermail/gmx-users/2007-April/027043.html The authors in the cited paper have created near-native structures as a

Re: [gmx-users] Energy minimization: problems with ramachanrad score

Without having actually read their paper... there's could easily be a kind of apples-and-oranges comparison going on. The local optimum resulting from a single EM using MM forcefields optimized for non-vacuum conditions on near-native folds in vacuo are being compared with (say) crystal