Re: [gmx-users] Dynamics cross correlation map
Hi Sukesh, I once put a version of g_covar that can calculate the correlations in the user contributions. Check if it's there or reply to me privately if you can't find it (though I'm on the road till Friday). Good luck, Ran On Wed, 24 Mar 2010 11:46:42 +0530 sukesh chandra gain suk...@atc.tcs.com wrote: Hi Tsjerk, Thank you for your reply. May be I was not very clear with my previous post. I am not looking for covariance / atomic covariances map (ie., covar.xpm/covara.xpm) which are generated by g_covar tool in GROMACS. I am particularly trying to get correlation map (example: http://www.pnas.org/content/102/4/994/F2.large.jpg, http://www.pnas.org/content/99/26/16597/F3.small.gif). I hope there is a difference between covariance matrix and correlation matrix. The correlated motions between two atoms is calculated as the magnitude of the co-relation coefficient between the atoms. In case of a system it can be assessed by examining the magnitude of all pairwise cross-correlation coefficients. The cross-correlation coefficient, C(i,j) for each pair of atoms i and j is calculated as: C(i,j) = delta r(i) * delta r(j) / sqrt sqr(delta r(i) ) . sqrt sqr(delta r(j) ) , where delta r(i) is the displacement from mean position of the ith atom and symbol represents the time average. This function returns a matrix of all atom-wise cross-correlations whose elements, C(i,j), may be displayed in a graphical representation frequently termed a dynamical cross-correlation map, or DCCM. If C(i,j) = 1 the fluctuations of atoms i and j are completely correlated, if C(i,j) = -1 the fluctuations of atoms i and j are completely anticorrelated and if C(i,j) = 0 the fluctuations of i and j are not correlated. Now my query is there any tool like g_correlation (http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/GeneralizedCorrelations/index.html) by which I can get the cross-correlation matrix from covariance matrix or directly from trajectory file. Ref:1. Hünenberger PH, Mark AE, van Gunsteren WF; Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations; JMB 1995; 252:492-503 2. Oliver F. Lange, H. Grubmüller; Generalized Correlation for Biomolecular Dynamics; Proteins 2006; 62:1053-1061 Thank You, Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- 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 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/mailing_lists/users.php -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Skype: ran.friedman -- -- 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 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/mailing_lists/users.php
Re: [gmx-users] Assembling a good simulation starting point
Hello John, How large was the force after EM? Large forces often results in systems that explode during the simulation. Also, did you minimise with or without solvent? You assessment seems correct - the initial structure wasn't minimised and the tools of the trade are trying different conformations, minimising in vacuo at first and using other modelling tools before Gromacs. Also, read a bit in the mailing list and search the literature for similar studies. Good luck, Ran On Thu, 18 Feb 2010 19:08:11 -0800 (PST) John Ladasky blind.watchma...@yahoo.com wrote: Hello everyone, I'm a fairly new GROMACS user. I'm running GROMACS 4.0.5 on top of Ubuntu Linux 9.10. I am still learning a lot. I just tried to set up my first fairly complex simulation, and it failed. I have a protein of interest, a beta barrel with a hydrophobic, ligand-binding interior. I am interested in making mutations to this protein, with the goal of getting it to bind to a rather different ligand than the one it normally binds. The way that I propose to go about studying this problem is to construct a partially-unfolded version of the protein structure, add my ligand of interest, and then run an energy minimization. My first naive attempt to construct the partially-unfolded protein was not successful. I knew that it might have problems, but I tried it anyway. Using Biopython, I rotated the atomic coordinates so that the beta barrel was parallel to an axis. Then I simply pulled all of the atoms 3 Angstroms away from the axis. Finally, I inserted my ligand. Visually, inspecting the starting structure with PyMol, I didn't see anything egregious. However, I could have some unwanted close contacts. I got a few long bond warnings from pdb2gmx, but I persisted. I got through genbox, editconf, and my first grompp sucessfully. But then when I tried the first, position-restrained energy minimization, it aborted with too many LINCS warnings. I blew the system up. These LINCS warnings could come from close contacts, or from large forces in over-stretched bonds which resulted from my crude approach to expanding the protein structure. Whatever the cause, I need a smarter way to start. I am open to ANY suggestions! What I THINK I might want to do is to manipulate the starting structure in a more natural way. For example, selecting some peptide bonds in the beta turns, and changing their angles. A program which allows me to manipulate structures, and not just simulate natural forces, is what I think I need. Surely, people who have used GROMACS will have faced problems simliar to mine. Thanks for your advice! John Ladasky -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Skype: ran.friedman -- -- 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 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/mailing_lists/users.php
Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones
Dear Josmar, As for the GROMOS FF, I've included a link to the paper describing the most recent (AFAIK) version of the FF in one of the recent mailing list massages. Good luck, Ran On Sat, 18 Apr 2009 15:56:11 -0400 Justin A. Lemkul jalem...@vt.edu wrote: Josmar R. da Rocha wrote: Dear Ran, Thanks for answering and sorry to take so long to reply. After your response I went seach for more information about that. What I read here in the list is that some people uses antechamber to generate am1-bcc charges (or RESP charges using Gaussian program) and convert the output files to a .top file (using the amb2gmx.pl script) that can be used in gromacs, however, nobody says the kind of ff they intend to use that charges with. Do these type of charges can also be used with Gromos96 ff ( 43a1)? Thanks in advance! The amb2gmx was created to handle AMBER-to-GROMACS conversion. It is unlikely that it would be useful for ffG43a1. Since 43a1 is a united-atom force field, you have to compensate for the fact that nonpolar hydrogen atoms are absent. Furthermore, quantum charge calculation is not a necessary component of Gromos96 parameter derivation. See, for example: http://wiki.gromacs.org/index.php/Parameterization -Justin Regards, Josmar Rocha --- Em *sex, 27/3/09, Ran Friedman, Biochemisches Inst. /r.fried...@bioc.uzh.ch/* escreveu: De: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch Assunto: Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones Para: bije...@yahoo.com.br, Discussion list for GROMACS users gmx-users@gromacs.org Data: Sexta-feira, 27 de Março de 2009, 17:35 Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with the same chemical moieties or use the same approach as reported in the relevant manuscripts. Some software packages can also be used - these are mostly proprietary and not so easy to use. Once you derive the parameters, it's a good idea to make some test runs of the ligands and see if they behave as expected before you actually run a simulation with the protein. For example, if a conjugate ring system isn't planar something may be wrong in the setting. There's no easy solution - this is why it's considered an advanced topic. It is, however, very important. I've encountered a ligand that leaves its binding site during a simulation due to wrong parameters (in this case, the protonation of a protein side chain - FEBS 581, Pages 4120-4124, 2007). Hope that helped, Ran On Fri, 27 Mar 2009 12:22:01 -0700 (PDT) Josmar R. da Rocha bije...@yahoo.com.br wrote: Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. Verli pointed out the use of semi-empirical methods such as RM1 in cases not involving simulations with sulphate or phosphate groups (what is not my case) and the use of QM methods with the 6-31G** basis set, for example, to obtain robust charges (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the other hand Dr. Mobley defined as a a bad idea to compute charges for an all-atom case using QM and then try to convert these to a united atom force field. Other users advice that the best charges are that compatible with the force field parametrization (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman suggested that to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential in order to make it less sensitive to small changes in the geometry of the molecule may give good results (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. Lemkul stressed the need for charges refinement to reproduce experimentally-observed behavior while trying to use QM charges with Gromos ff. since Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. Few examples of protein-ligand studies using Gromacs and Gromos96 ff that I have access (from literature) seem to treat it as take
Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones
Hi, I've recently used OPLS-AA for a similar calculation. It has the advantage that many atom types are already defined in Gromacs and that QM-based calculations give you reasonable charges. Note that it may take considerable simulation time (tens of ns) to discriminate between similar docked poses of the same molecule, though MD can give you a hint. If things were easier docking programs would do a better job. Ran. On Wed, 01 Apr 2009 00:12:31 -0600 Lucio Ricardo Montero Valenzuela lucio...@ibt.unam.mx wrote: So it 's better to switch to the OPLS forcefield if I want to compute the charges?. How can I implement the OPLS-UA if my gromacs (version 3.3) only includes the OPLS-AA? Mensaje citado por Justin A. Lemkul jalem...@vt.edu: Lucio Montero wrote: How about MOPAC to calculate the charges for 3-methyladenine (this molecule has a charge +1) for using the G43a1 force field?. That may not be a bad place to start, but any parameters applied to a Gromos molecule have to reproduce condensed phase thermodynamic observables. Empirical fitting of the initial parameters may be required. Refer to the primary literature. The reference for the 53a5 and 53a6 parameter sets are published in JCC, which may provide you with some useful information. -Justin -- From: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch Sent: Friday, March 27, 2009 2:35 PM To: bije...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRGassignedones Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with the same chemical moieties or use the same approach as reported in the relevant manuscripts. Some software packages can also be used - these are mostly proprietary and not so easy to use. Once you derive the parameters, it's a good idea to make some test runs of the ligands and see if they behave as expected before you actually run a simulation with the protein. For example, if a conjugate ring system isn't planar something may be wrong in the setting. There's no easy solution - this is why it's considered an advanced topic. It is, however, very important. I've encountered a ligand that leaves its binding site during a simulation due to wrong parameters (in this case, the protonation of a protein side chain - FEBS 581, Pages 4120-4124, 2007). Hope that helped, Ran On Fri, 27 Mar 2009 12:22:01 -0700 (PDT) Josmar R. da Rocha bije...@yahoo.com.br wrote: Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. Verli pointed out the use of semi-empirical methods such as RM1 in cases not involving simulations with sulphate or phosphate groups (what is not my case) and the use of QM methods with the 6-31G** basis set, for example, to obtain robust charges (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the other hand Dr. Mobley defined as a a bad idea to compute charges for an all-atom case using QM and then try to convert these to a united atom force field. Other users advice that the best charges are that compatible with the force field parametrization (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman suggested that to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential in order to make it less sensitive to small changes in the geometry of the molecule may give good results (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. Lemkul stressed the need for charges refinement to reproduce experimentally-observed behavior while trying to use QM charges with Gromos ff. since Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. Few examples of protein-ligand studies using Gromacs and Gromos96 ff that I have access (from literature) seem to treat it as take it for granted issue (any reference with a more detailed description would be welcome :-)). Despite reading on this topic I could not compile all the information in a clear and objective way (may be because I'm in the wrong track). Let ask you some question
Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones
Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with the same chemical moieties or use the same approach as reported in the relevant manuscripts. Some software packages can also be used - these are mostly proprietary and not so easy to use. Once you derive the parameters, it's a good idea to make some test runs of the ligands and see if they behave as expected before you actually run a simulation with the protein. For example, if a conjugate ring system isn't planar something may be wrong in the setting. There's no easy solution - this is why it's considered an advanced topic. It is, however, very important. I've encountered a ligand that leaves its binding site during a simulation due to wrong parameters (in this case, the protonation of a protein side chain - FEBS 581, Pages 4120-4124, 2007). Hope that helped, Ran On Fri, 27 Mar 2009 12:22:01 -0700 (PDT) Josmar R. da Rocha bije...@yahoo.com.br wrote: Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. Verli pointed out the use of semi-empirical methods such as RM1 in cases not involving simulations with sulphate or phosphate groups (what is not my case) and the use of QM methods with the 6-31G** basis set, for example, to obtain robust charges (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the other hand Dr. Mobley defined as a a bad idea to compute charges for an all-atom case using QM and then try to convert these to a united atom force field. Other users advice that the best charges are that compatible with the force field parametrization (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman suggested that to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential in order to make it less sensitive to small changes in the geometry of the molecule may give good results (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. Lemkul stressed the need for charges refinement to reproduce experimentally-observed behavior while trying to use QM charges with Gromos ff. since Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. Few examples of protein-ligand studies using Gromacs and Gromos96 ff that I have access (from literature) seem to treat it as take it for granted issue (any reference with a more detailed description would be welcome :-)). Despite reading on this topic I could not compile all the information in a clear and objective way (may be because I'm in the wrong track). Let ask you some question that I find would help me to make my ideas more clear: 1-am I overestimating the importance of ligand charges in such a simple study of protein-small molecule (containg charged Phosphate groups) complex? or 1.1-The only way to test for this is doing many different simulation on the same system using different type of computed charges to see what happen? 2-How could I try to choose a method to obtain reasonable charges based on the reproduction of experimentally-observed behavior if I do not have experimental data for my system? 3-I also would like to know from users dealing with protein-ligand interactions studies what do you consider a good approach to address this problem? Based on what I read I'd have a tendency to use HF/6-31G** ESP derived charges (with necessary changes as to make it united-atom charges and scaling that to a integer number for each group). Please, let me know if that strategy would be as good as a disaster! Thank you very much for the attention. Josmar Rocha Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com ___ 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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Peptide aggregation
Dear Leon, Note that you can already use g_clustsize to check the aggregates. I'll contact you off list next week with the modified version. Ran On Fri, 19 Sep 2008 17:13:02 +0100 Léon Salgado [EMAIL PROTECTED] wrote: Dear Dr. Ran Friedman Would you please be so kind to send me your version, to calculate then the rgyr of the largest aggregate. The box was built with a layer of 1.2 nm around the solute (editconf -d 1.2). Leon Ran Friedman wrote: Dear Leon, You can try to use g_clustsize to get the aggregates. I have a version that can calculate the gyration radius of the largest aggregate, but this would work only if your box is big enough and I haven't tried it with rhombic dodecahedron boxes. Ran. Léon Salgado wrote: Dear gmx users I did some simulations of multimers (peptides) in rhombic dodecahedron boxes. In the initial configuration of the system, the peptides are close of each other in the center of the box. My aim to see if the peptides do aggregate during the trajectory or if they tend to stay apart. A rough estimate can be taken from the gyration radius for all the peptides together. Already did a trjconv -pbc nojump pre-treatment on the trajectory, before calculating the Rgyr. The gyration.xvg plots sometimes do show abrupt jumps, and this is surely due to boundary effects, if I correctly understood the PBC idea. If a peptide approaches the boundary, it appears on the opposite side, thus rgyr will show a false sudden increase. In fact, the peptide could be closer to the rest of the other peptide molecule(s). Thus my question is: how to deal with peptide clusters that span over the periodic boundaries? A similar question was done by Singh: http://www.gromacs.org/pipermail/gmx-users/2007-January/025474.html and it was suggested by Chris Neale to pre-process the trajectory (see http://www.gromacs.org/pipermail/gmx-users/2007-January/025481.html) with: trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump but I'm getting infinite loops on the -pbc cluster treatment, same as reported by Chris (http://www.gromacs.org/pipermail/gmx-users/2008-July/035343.html). Best, Léon ___ 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. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Skype: ran.friedman -- ___ 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. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Neutralizing the total charge of the system in vacuum
Hello, You can add a few ions manually or use genbox. However, it's probably better to use a vacuum force field and have your peptide uncharged for vacuum simulations. Any ions you add will have a very strong interaction with the peptide. I assume you have a good reason to simulate in vacuo - the mailing list archives give many reasons why it's not advised. Ran. On Sat, 24 Nov 2007 19:47:43 +0200 OZGE ENGIN [EMAIL PROTECTED] wrote: Hi all, I am performing a simulation in vacuum. The peptide has nonzero charge, so I attempted to neutralize the total charge via genion;however as it is known, it asks for a continuous group for replacing, but I have no solvent molecules for the replacement. How can I neutralize the total charge while performing simulations in vacuum? Thanks in advance Oz. ___ 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. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6354493 Skype: ran.friedman -- ___ 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. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] quasiharmonic eigenvalue units / Schlitter entropy
Dear Marcin, You can contact me off list for a script that calculates the QH entropies from the output of g_covar. Also, IIRC there should be a version of g_covar that already does it somewhere (CVS-?). Ran. On Wed, 31 Oct 2007 17:40:45 + Marcin Krol [EMAIL PROTECTED] wrote: Dear All, Sorry for the repeated question, but I'm a bit lost when I want to get frequencies of modes from quasiharmonic analysis done with g_covar. From what I understood in QH omega = sqrt(kT/lambda), where omega is the radial frequency, k - Boltzmann const, T-temp, and lambda is the eigenvalue. In order to get the units right lambda needs to be in length^2*mass units. Is it nm^2*amu? I need the frequencies to calculate entropy estimate from QH analysis. However, another way of getting the entropy estimate would be to get it from Schlitter formula. Then, I wouldn't need to diagonalize the covariance matrix. Is there a way to request the calculation of Schlitter entropy after the covariance matrix is calculated, but before g_covar starts diagonalization? Thanks in advance marcin -- Dr Marcin Krol Biomolecular Modelling Laboratory Cancer Research UK e-mail: [EMAIL PROTECTED] AND Department of Bioinformatics Collegium Medicum Jagiellonian University e-mail: [EMAIL PROTECTED] ___ 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. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6354493 Skype: ran.friedman -- ___ 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. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
