[gmx-users] Dynamics cross correlation map
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
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
[gmx-users] Re:x2top
Charges... Hmmm... I think you have incorrect data types passed to x2top. Vitaly I think the result cannot be trusted because the total charge is 1.2, which seems impossible. I just used the result calculated by Material Studio and I used the value of charge on the internal atoms. The atoms in surface have different charges. I have to change the charge by hand. P.S. -pbc or -nopbc is depend on if you will use Periodical Boundary Condition. My pdb is a SiO2 sphere, so I used -nopbc Di Cheng -- 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
[gmx-users] extract subsystem energy: problem with mdrun -rerun and LJ(SR)
Dear all, I have performed a MD of a polymer chain interacting on a carbon nanotube using gromacs 4.0.7. I need to evaluate the potential energy of the polymer alone, during the dynamic, so to compare with its potential energy in vacuo. During the dynamic, the CNT was frozen, and I used exclusions groups to avoid to calculate CNT CNT non bonding interactions (I assume the bonds and angles potentials are computed anyway). Looking at the mailing list, I have used the following method: 1) use make_ndx to create a group system containing only the atoms for the polymer 2) Create a new simulation file:tpbconv -s original.tpr -n index.ndx -o rerun.tpr 3) adjust the trajectory according to the new simulation file: trjconv -f totaltrj.xtc -n index.ndx -s rerun.tpr -o rerun.xtc 4) analyze the trajectory: mdrun -s rerun.tps -rerun rerun.xtc everything is performed without errors, but, when I use g_energy to evaluate the energy of the polymer, I get something like: Statistics over 1501 steps [ 0. thru 3.0020 ps ], 7 data sets All averages are over 15001 frames Energy Average RMSD Fluct. Drift Tot-Drift -- - Angle 1630.1861.535661.0703 -0.000872146 -26.1644 Ryckaert-Bell. 233.04945.135834.5826 -0.00334919 -100.476 LJ-14 669.90720.079719.9169 -0.000294607 -8.8382 Coulomb-14 637.18716.292116.1707 0.000229164 6.87492 LJ (SR) 0 0 0 0 0 Coulomb (SR) 0 0 0 0 0 Potential 3170.3384.065475.4238 -0.00428678 -128.603 The question is: why the short range lennard-jones and short range coulombic interactions are zero? those are the usual option from 1 to 8: 2 Angle3 Ryckaert-Bell. 4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 Coulomb-(SR) 8 Potential They are present for the orginal dynamic on CNT as well as in the dynamic in vacuo. hope in some answers. Thanks Andrea -- Dr. Andrea Minoia Chemistry of Novel Materials Uneversity of Mons, UMONS Parc Initialis, Avenue Copernic 1 B-7000 Mons, Belgium Mail: mino...@averell.umh.ac.be Tel: +32 65 373859 Fax: +32 65 373861 -- 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] extract subsystem energy: problem with mdrun -rerun and LJ(SR)
On 24/03/2010 7:34 PM, Andrea Minoia wrote: Dear all, I have performed a MD of a polymer chain interacting on a carbon nanotube using gromacs 4.0.7. I need to evaluate the potential energy of the polymer alone, during the dynamic, so to compare with its potential energy in vacuo. During the dynamic, the CNT was frozen, and I used exclusions groups to avoid to calculate CNT CNT non bonding interactions (I assume the bonds and angles potentials are computed anyway). Looking at the mailing list, I have used the following method: 1) use make_ndx to create a group system containing only the atoms for the polymer 2) Create a new simulation file:tpbconv -s original.tpr -n index.ndx -o rerun.tpr 3) adjust the trajectory according to the new simulation file: trjconv -f totaltrj.xtc -n index.ndx -s rerun.tpr -o rerun.xtc 4) analyze the trajectory: mdrun -s rerun.tps -rerun rerun.xtc everything is performed without errors, but, when I use g_energy to evaluate the energy of the polymer, I get something like: Statistics over 1501 steps [ 0. thru 3.0020 ps ], 7 data sets All averages are over 15001 frames Energy Average RMSD Fluct. Drift Tot-Drift -- - Angle 1630.1861.535661.0703 -0.000872146 -26.1644 Ryckaert-Bell. 233.04945.135834.5826 -0.00334919 -100.476 LJ-14 669.90720.079719.9169 -0.000294607-8.8382 Coulomb-14 637.18716.292116.1707 0.000229164 6.87492 LJ (SR) 0 0 0 0 0 Coulomb (SR) 0 0 0 0 0 Potential 3170.3384.065475.4238 -0.00428678 -128.603 The question is: why the short range lennard-jones and short range coulombic interactions are zero? those are the usual option from 1 to 8: 2 Angle3 Ryckaert-Bell. 4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 Coulomb-(SR) 8 Potential They are present for the orginal dynamic on CNT as well as in the dynamic in vacuo. hope in some answers. Thanks In the absence of information about your ensemble (from your .mdp file or a description, hint hint) I'd guess it's because you've excluded all the non-bonded interactions for which you had non-zero parameters defined. Mark -- 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] extract subsystem energy: problem with mdrun -rerun and LJ(SR)
Mark, thank you for the fast reply. My original mdp, the one I used to run the dynamics is nstcgsteep = 1000 nbfgscorr= 10 emstep = 0.02 emtol= 10 dt = 0.002 nsteps = 1500 comm-mode= none nstcomm = 1 comm_grps= system nstxout = 1000 nstvout = 1000 nstfout = nstlog = 1000 nstenergy= 1000 nstxtcout= 1000 xtc_grps = system energygrps = CNT pcl nstlist = 10 ns_type = grid pbc = xyz rlist= 1.5 coulombtype = cut-off rcoulomb = 1.5 vdwtype = cut-off rvdw = 1.5 periodic_molecules = yes tcoupl = nose-hoover tc-grps = system tau_t= 0.5 ref_t= 300 Pcoupl = no pcoupltype = isotropic tau_p= 5.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = no gen_temp = 300 gen_seed = -1 constraints = all-bonds constraint_algorithm = LINCS lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 freezegrps = CNT freezedim= Y Y Y nwall= 0 wall_type= 9-3 wall_r_linpot= -1 wall_atomtype= wall_density = wall_ewald_zfac = 3 ewald_geometry = 3d energygrp_excl = CNT CNT with this I have created, of course the tpr used to run the dynamic: runmd.tpr. With make_ndx, I have an index file containing only the pcl group. using this index file, i have created the new tpr, rerun.tpr, from the original runmd.tpr file using tpbconv. as far as I see, the only exclusion is for the CNT CNT groups (last line of the mdp file above). a gmxdump of rerun.tpr gives me this info about groups (at the end of the file) Group statistics T-Coupling : 756 (total 756 atoms) Energy Mon. : 756 0 0 (total 756 atoms) Acceleration: 756 (total 756 atoms) Freeze : 756 0 (total 756 atoms) User1 : 756 (total 756 atoms) User2 : 756 (total 756 atoms) VCM : 756 (total 756 atoms) XTC : 756 (total 756 atoms) Or. Res. Fit: 756 (total 756 atoms) QMMM: 756 (total 756 atoms) If this is not helping you, please can you tell me what else you need? Again, thanks. cheers, Andrea In the absence of information about your ensemble (from your .mdp file or a description, hint hint) I'd guess it's because you've excluded all the non-bonded interactions for which you had non-zero parameters defined. Mark -- 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 -- Dr. Andrea Minoia Chemistry of Novel Materials Uneversity of Mons, UMONS Parc Initialis, Avenue Copernic 1 B-7000 Mons, Belgium Mail: mino...@averell.umh.ac.be Tel: +32 65 373859 Fax: +32 65 373861 -- 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] Dynamics cross correlation map
Hi Sukesh, Great. This makes things much clearer. So basically what you'd need to do is to divide each i,j-th element of the covariance matrix you obtained (covar.dat) by the sqrt of the ii-th and jj-th diagonal element. That will commonly turn a covariance matrix into a correlation matrix. But, that also happens to be what the modified version of g_covar provided by Ran does. I think it's still on the contributions page. Just one more thing, the generalized correlation of Lange and Grubmueller is a bit of a different thing. Might also be handy though. In stead of calculating the correlation as the normalized product moment, they have a similarity parameter that measures how close the actual distribution of measurements is to the one you'd get if the measurements were uncorrelated (mutually independent). This compensates for non-linear relationships between variables. Cheers, Tsjerk On Wed, Mar 24, 2010 at 7:16 AM, 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 list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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] make ghost atom
I'm not sure if this helps, but have you tried link/ dummy atoms like you use them for QMMM? For dummies add a line to ff***nb.itp where you define them to have neither charge nor weight (also 0 for LJ-pot). Then add them to your topology-file. Check out http://www.gromacs.org/Documentation/How-tos/QMMM Quoting Park, Jae Hyun nmn pa...@ornl.gov: Dear all, I would like to change a specific atom into a ghost particle (no interaction with system) after some time (for example, 1ns). Is there any way to implement it in GROMACS? If I need change the code, what file do I have to look at? I would deeply appreciate any comments. Jae H. Park Jae Hyun Park, Ph.D. Physics Division Oak Ridge National Laboratory P.O. Box 2008, MS-6372 Oak Ridge, TN 37831 Phone (865) 241-1482 E-mail pa...@ornl.gov -- 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] extract subsystem energy: problem with mdrun -rerun and LJ(SR)
I found something: apparently, I need to remove the energygrp_excl = CNT CNT from the original mdp, generate a new tpr with this modified mdp and grompp, and then use tpbconv to create the simulation file for the subsystem. my energy groups are still CNT and pcl and now g_energy gives something like this: LJ (SR)-749.54682.968663.7099 0.00613714 184.114 Potential2214.789.275189.1628 0.000516773 15.5032 LJ-SR:pcl-pcl 0 0 0 0 0 but still, LJ-SR:pcl-pcl is 0... should not be the same as LJ(SR)?... does not make too much sense. Summarizing what i did: 1) edit the mdp file, remove the groups in energygrp_excl, even if not used in the subsytem Just to clarify, comparing the new mdp with that posted before, the only difference is: energygrp_excl = --- energygrp_excl = CNT CNT 2) create the index file for the subsystem 3) rerun grompp to create the new tpr for all the system, without energygrp_excl 4) use the new tpr with tpbconv to create the simulation file for the subsystem 5) adjust the trajectory 6) run mdrun -rerun andrea -- Dr. Andrea Minoia Chemistry of Novel Materials Uneversity of Mons, UMONS Parc Initialis, Avenue Copernic 1 B-7000 Mons, Belgium Mail: mino...@averell.umh.ac.be Tel: +32 65 373859 Fax: +32 65 373861 -- 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
[gmx-users] Query regarding toplogy of Manganese ion in protein
Hello, I have protein in my protein, for which i want to run MD simulation. Could you please help me to know how to generate topology file for Manganese and which force field to use, as none of the force field in Gromacs supports Mn ion. Please Help Regards -- Sonali Dhindwal The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- 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
[gmx-users] Re: Query regarding toplogy of Manganese ion in protein
Hello, I have a Manganese ion in my protein, for which i want to run MD simulation. Could you please help me to know how to generate topology file for Manganese and which force field to use, as none of the force field in Gromacs supports Mn ion. Please Help Regards -- Sonali Dhindwal --- On Wed, 24/3/10, sonali dhindwal sonali11dhind...@yahoo.co.in wrote: From: sonali dhindwal sonali11dhind...@yahoo.co.in Subject: Query regarding toplogy of Manganese ion in protein To: gmx-users@gromacs.org Date: Wednesday, 24 March, 2010, 5:35 PM Hello, I have protein in my protein, for which i want to run MD simulation. Could you please help me to know how to generate topology file for Manganese and which force field to use, as none of the force field in Gromacs supports Mn ion. Please Help Regards -- Sonali Dhindwal Your Mail works best with the New Yahoo Optimized IE8. Get it NOW!. Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/-- 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] Query regarding toplogy of Manganese ion in protein
sonali dhindwal wrote: Hello, I have protein in my protein, for which i want to run MD simulation. Could you please help me to know how to generate topology file for Manganese and which force field to use, as none of the force field in Gromacs supports Mn ion. Parameterization is considered a very advanced task, and generating good parameters for a transition metal is especially challenging. See here: http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species Parameters for Mn are available for the AMBER force fields, which can be incorporated into Gromacs with the ffamber ports. The reference for Mn can be found at: http://www.pharmacy.manchester.ac.uk/bryce/amber#ion -Justin Please Help Regards -- Sonali Dhindwal Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://in.rd.yahoo.com/tagline_ie8_new/*http://downloads.yahoo.com/in/internetexplorer/. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Query regarding toplogy of Manganese ion in protein
Thanks for your help I hope it will work. Regards -- Sonali Dhindwal --- On Wed, 24/3/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Query regarding toplogy of Manganese ion in protein To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, 24 March, 2010, 5:44 PM sonali dhindwal wrote: Hello, I have protein in my protein, for which i want to run MD simulation. Could you please help me to know how to generate topology file for Manganese and which force field to use, as none of the force field in Gromacs supports Mn ion. Parameterization is considered a very advanced task, and generating good parameters for a transition metal is especially challenging. See here: http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species Parameters for Mn are available for the AMBER force fields, which can be incorporated into Gromacs with the ffamber ports. The reference for Mn can be found at: http://www.pharmacy.manchester.ac.uk/bryce/amber#ion -Justin Please Help Regards -- Sonali Dhindwal Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://in.rd.yahoo.com/tagline_ie8_new/*http://downloads.yahoo.com/in/internetexplorer/. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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 The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- 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] Query regarding toplogy of Manganese ion in protein
On 24/03/2010 11:37 PM, sonali dhindwal wrote: Thanks for your help I hope it will work. Better than just hoping is design a small test case to see if the parameters are vaguely suitable for *your* purpose - and read up on how they were parameterized and for what purpose... Your problem could easily be too large in scope for someone without years of MD experience. Mark --- On *Wed, 24/3/10, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Query regarding toplogy of Manganese ion in protein To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, 24 March, 2010, 5:44 PM sonali dhindwal wrote: Hello, I have protein in my protein, for which i want to run MD simulation. Could you please help me to know how to generate topology file for Manganese and which force field to use, as none of the force field in Gromacs supports Mn ion. Parameterization is considered a very advanced task, and generating good parameters for a transition metal is especially challenging. See here: http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species Parameters for Mn are available for the AMBER force fields, which can be incorporated into Gromacs with the ffamber ports. The reference for Mn can be found at: http://www.pharmacy.manchester.ac.uk/bryce/amber#ion -Justin Please Help Regards -- Sonali Dhindwal Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://in.rd.yahoo.com/tagline_ie8_new/*http://downloads.yahoo.com/in/internetexplorer/. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org /mc/compose?to=gmx-us...@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 /mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php The INTERNET now has a personality. YOURS! See your Yahoo! Homepage http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/. -- 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
[gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations
Dear gromacs users: How to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations; for example, software or script using, how to reconstruct PMF in detail? thank you very much! -- 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] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations
xi zhao wrote: Dear gromacs users: How to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations; for example, software or script using, how to reconstruct PMF in detail? thank you very much! http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
[gmx-users] how to analye a single structure (NMR or X-ray) by PCA?
Dear sir : I want to analye a collective motions of a single structure by PCA , for example, how to choose reference structure using g_covar; how to show its position in 2D-projection (conformational space)? thank you very much! -- 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] how to analye a single structure (NMR or X-ray) by PCA?
xi zhao wrote: Dear sir : I want to analye a collective motions of a single structure by PCA , for example, how to choose reference structure using g_covar; how to show its position in 2D-projection (conformational space)? thank you very much! There have been several discussions on this topic (hint: search the list archive), one even in recent days: http://lists.gromacs.org/pipermail/gmx-users/2010-March/049525.html Also, read g_covar -h for information about the algorithm. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations
dear Mr Justin A. Lemkul : I have read your tutorial ,it is suitable for umbrella sampling method, it is not for SMD, wham or g_wham can not be used! Thnak you! --- 10年3月24日，周三, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年3月24日,周三,下午9:58 xi zhao wrote: Dear gromacs users: How to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations; for example, software or script using, how to reconstruct PMF in detail? thank you very much! http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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 -- 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] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations
xi zhao wrote: dear Mr Justin A. Lemkul : I have read your _tutorial ,it is suitable for umbrella sampling method, it is not for SMD, wham or g_wham can not be used!_ _Thnak you!_ If you want to use SMD trajectories to calculate free energy changes, you will need Jarzynski's inequality and a large amount of sampling. I do not think such a method is implemented in Gromacs; you may have to write your own scripts to do this. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年3月24日，周三, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年3月24日,周三,下午9:58 xi zhao wrote: Dear gromacs users: How to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations; for example, software or script using, how to reconstruct PMF in detail? thank you very much! http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@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 http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] how to analye a single structure (NMR or X-ray) by PCA?
Hi, Now that particular reference was not a very suitable one for this question :) The proper reply here is: There are no collective motions in a single structure, period! Do some background reading on PCA, and some more on PCA as applied to MD simulations. There is some information in the manual, there are plenty of papers and there is a bit of it in the tutorial at http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html. And there is indeed a lot said on the mailing list too. Also note that PCA is not an easy subject. Cheers, Tsjerk On Wed, Mar 24, 2010 at 3:06 PM, Justin A. Lemkul jalem...@vt.edu wrote: xi zhao wrote: Dear sir : I want to analye a collective motions of a single structure by PCA , for example, how to choose reference structure using g_covar; how to show its position in 2D-projection (conformational space)? thank you very much! There have been several discussions on this topic (hint: search the list archive), one even in recent days: http://lists.gromacs.org/pipermail/gmx-users/2010-March/049525.html Also, read g_covar -h for information about the algorithm. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- 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] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations
Dear Mr Justin A. Lemkul : Thank you for your advice, can you give more suggetions? Thank you very much! --- 10年3月24日，周三, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2010年3月24日,周三,下午10:10 xi zhao wrote: dear Mr Justin A. Lemkul : I have read your _tutorial ,it is suitable for umbrella sampling method, it is not for SMD, wham or g_wham can not be used!_ _Thnak you!_ If you want to use SMD trajectories to calculate free energy changes, you will need Jarzynski's inequality and a large amount of sampling. I do not think such a method is implemented in Gromacs; you may have to write your own scripts to do this. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年3月24日，周三, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年3月24日,周三,下午9:58 xi zhao wrote: Dear gromacs users: How to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations; for example, software or script using, how to reconstruct PMF in detail? thank you very much! http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@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 http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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 -- 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] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations
Dear Mr Justin A. Lemkul : In fact, please read the document http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-513/paper06.pdf, the document shows the PMF can be reconstructed from the SMD, why? thank you! --- 10年3月24日，周三, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2010年3月24日,周三,下午10:10 xi zhao wrote: dear Mr Justin A. Lemkul : I have read your _tutorial ,it is suitable for umbrella sampling method, it is not for SMD, wham or g_wham can not be used!_ _Thnak you!_ If you want to use SMD trajectories to calculate free energy changes, you will need Jarzynski's inequality and a large amount of sampling. I do not think such a method is implemented in Gromacs; you may have to write your own scripts to do this. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年3月24日，周三, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2010年3月24日,周三,下午9:58 xi zhao wrote: Dear gromacs users: How to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations; for example, software or script using, how to reconstruct PMF in detail? thank you very much! http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@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 http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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 -- 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] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations
Ah, I can make some advertisement for my own work again. If you can do equilibrium simulations these will always be more efficient than non-equilibrium, as Justin also pointed out below. I have published a case where you can not (or not efficiently) do equilibrium simulations, because you don't know the end state, then non-equilibrium simulations are really useful, otherwise not: http://pubs.acs.org/doi/abs/10.1021/ma702070n Berk Date: Wed, 24 Mar 2010 10:48:18 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations xi zhao wrote: Dear Mr Justin A. Lemkul : In fact, please read the document http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-513/paper06.pdf, the document shows the PMF can be reconstructed from the SMD, why? I never disputed that fact. Please the post I just sent you. The conclusions of the paper indicate that umbrella sampling is more robust and costs less time, although, if conducted properly, SMD can yield similar results. -Justin thank you! 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年3月24日，周三, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations 收件人: Gromacs Users' List gmx-users@gromacs.org 日期: 2010年3月24日,周三,下午10:10 xi zhao wrote: dear Mr Justin A. Lemkul : I have read your _tutorial ,it is suitable for umbrella sampling method, it is not for SMD, wham or g_wham can not be used!_ _Thnak you!_ If you want to use SMD trajectories to calculate free energy changes, you will need Jarzynski's inequality and a large amount of sampling. I do not think such a method is implemented in Gromacs; you may have to write your own scripts to do this. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *10年3月24日，周三, Justin A. Lemkul /jalem...@vt.edu http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu 主题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations 收件人: Discussion list for GROMACS users gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org 日期: 2010年3月24日,周三,下午9:58 xi zhao wrote: Dear gromacs users: How to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations; for example, software or script using, how to reconstruct PMF in detail? thank you very much! http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please
[gmx-users] cutoff problem
Hi, I want to test different values of cutoff for vdw. However, in the list someone said cutoff = 0.9 for vdw was used for paramaterizing of Gromos force field, other values would cause error, and also there was someone saying that cutoff for vdw should be set to 1.4. Can someone make this question clear? Thanks a lot. Qian -- 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] cutoff problem
Qian Wang wrote: Hi, I want to test different values of cutoff for vdw. However, in the list someone said cutoff = 0.9 for vdw was used for paramaterizing of Gromos force field, other values would cause error, and also there was someone saying that cutoff for vdw should be set to 1.4. Can someone make this question clear? Thanks a lot. It is always helpful to post the URL's to the posts where you found this information. If your goal is to test different cutoff values, you should be able to sort out sources of error. Have a look at the original literature. For example, in the citation for the 53A5/53A6 parameter sets: ...the parameters used to describe the van der Waals interactions in the liquids perform well in combination with the (recently developed) aliphatic van der Waals parameters. All have now been parameterized with a cutoff of 1.4 nm. Furthermore, that paper describes the appropriate cutoffs for neighborsearching and short-range Coulombic interactions, although the latter is somewhat flexible in conjunction with PME, which was not used in the original derivation. -Justin Qian -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
[gmx-users] Re: Re: Re: g_bundle problem
Stefan Hoorman wrote: Stefan Hoorman wrote: Stefan Hoorman wrote: I have tried using g_bundle in order to analyse helix axes in my transmembran helices. I created two groups in my ndx file that included the alpha carbons of the first half of my helix and a second group for the alpha carbons for the second half. When I try using g_bundle the following error comes up: Fatal error: The size of one of your index groups is not a multiple of n What am I doing wrong? Not a clue - What is your exact command line? How many atoms are in each index group? The value of n is the number of parts into which the axes are divided and there are several criteria in the code that must be met, else you get this error. So without this information, the best guess is: some criterion is not being met. -Justin Thank you -- g_bundle analyzes bundles of axes - and therefore number of atoms each group have to be divisible by number of axes (entered by -na). And I suppose, you are interested in analyzing only one axis, don't you? Milan Well, the exact command line was : g_bundle -f md.xtc -s md.tpr -z -n bundle.ndx As for analyzing one axis, yes, that is true, I am only interested in analysing my helix principal axis. I have tried using different group sizes for the index group. I have tried using only carbon alpha for the first half and then for the second half (each had 15 alpha carbons), then I tried with all sorts of different groups, first five residues and last five residues, first fifteen residues and so on. All analysis came up with the same error. You're not setting the -na flag, which by default is zero. In the code, if the value from -na (int n) is = 0, you get the fatal error. Maybe the error message should be made more specific, so that users actually know what n is. You need to explicitly set a value for -na = 1. -Justin Right, thank you Justin, things worked out nicely now. I was able to calculatemy helix tilt with respect to the z axis. Would there be a way to calculate the tilt between two helix axes? I cannot simply calculate the tilt of each with respect to the z axis and subtract because the interhelical tilt does not depend only on the z axis. Can g_bundle give me that kind of information? It seems like it should: http://lists.gromacs.org/pipermail/gmx-users/2007-October/030415.html There are other programs that calculate angles, like g_sgangle and g_angle, both of which could potentially be used to calculate what you want. -Justin I have tried using g_sgangle, but the problem is that it does not calculate the principal axis of the helix. Since g_sgangle allows me to choose at maximum 3 atoms per analysis, it is quite difficult to perform such an analysis if one is to do this for 4 or five different systems and dimers. So, in this case, since g_bundle asks me to select a group of top and a group of bottom atoms, I would need to create an index group with my first group (top) being the top residues of both my helices and the second group being the bottom residues of my helices. Or would I create a first group for my first helix and a second group for my second helix? -- 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] Re: Re: Re: g_bundle problem
Stefan Hoorman wrote: snip I have tried using g_sgangle, but the problem is that it does not calculate the principal axis of the helix. Since g_sgangle allows me to choose at maximum 3 atoms per analysis, it is quite difficult to perform such an analysis if one is to do this for 4 or five different systems and dimers. So, in this case, since g_bundle asks me to select a group of top and a group of bottom atoms, I would need to create an index group with my first group (top) being the top residues of both my helices and the second group being the bottom residues of my helices. Or would I create Per the documentation, that sounds right. The program reads two index groups and divides both of them in -na parts. The centers of mass of these parts define the tops and bottoms of the axes. -Justin a first group for my first helix and a second group for my second helix? -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
[gmx-users] Semi-isotropic pressure coupling.
Hello all, I have a simulation running for a hydrate (with CO2) and water in contact with each other. I run the simulation at 280K at which the hydrate melts and finally the system is just liquid water with CO2 in it. However, as the simulation proceeds the box begins to expand in the z-direction and decreases in the x-y direction considerably. Initially the box has 4.8x4.8x9.6 nm^3 dimension. After the hydrate melts (the volume fluctuates more) and is fine for another 10 ns but after that the dimensions in the x-y direction decrease to 2.5 nm and z-dimension increases to 35 nm. At this point the simulation crashes since my cut-off distance are 1.2 nm. I am using semi-isotropic pressure coupling but the pressure in the x-y direction and z-direction are the same (=30.5 bar) and so is the compressibility (=4.5e-5). I am using Parrinello-Rahman pressure coupling and Nose-Hoover thermostat. The CO2 and water molecules are rigid and shake is used to maintain their geometry. The simulation time step is 2 fs. Can someone tell me why such a thing happens? I have pasted my mdp file for completeness. MDP File: title = CO2 hydrate + water ; a string cpp = /lib/cpp ; c-preprocessor dt = 0.002; time step nsteps = 2500; number of steps nstcomm = 10 ; reset c.o.m. motion nstxout = 2; write coords nstvout = 2; write velocities nstlog= 25000; print to logfile nstenergy = 500 ; print energies xtc_grps= OW_HW1_HW2_CO2 nstxtcout = 500 nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw= 1.2 ; cut-off for vdw rcoulomb = 1.2 ; cut-off for coulomb rlist = 1.2 ; cut-off for coulomb DispCorr = EnerPres Tcoupl = Nose-Hoover ref_t = 300 tc-grps = System tau_t = 0.5 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic; pressure geometry tau_p = 1.0 1.0; p-coupoling time compressibility = 4.5e-5 4.5e-5 ; compressibility ref_p = 30.5 30.5 ; ref pressure gen_vel = yes ; generate initial vel gen_temp= 200 ; initial temperature gen_seed= 372340 ; random seed constraint_algorithm = shake constraints = all-bonds Thanks a lot Sapna -- 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
[gmx-users] Re: cutoff problem
Hi, I want to test different values of cutoff for vdw. However, in the list someone said cutoff = 0.9 for vdw was used for paramaterizing of Gromos force field, other values would cause error, and also there was someone saying that cutoff for vdw should be set to 1.4. Can someone make this question clear? Thanks a lot. The common rule for all FFs is to set the LJ-cutoff around 2.5*sigma(LJ12-6). In fact, you'll get about 0.9 nm for the most objects. I see nothing terrible if you use, say, 1.4 nm just because the difference will be negligible. Just test it. :) -- Dr. Vitaly Chaban -- 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
[gmx-users] Re: Re: Re: Re: g_bundle problem
Stefan Hoorman wrote: snip I have tried using g_sgangle, but the problem is that it does not calculate the principal axis of the helix. Since g_sgangle allows me to choose at maximum 3 atoms per analysis, it is quite difficult to perform such an analysis if one is to do this for 4 or five different systems and dimers. So, in this case, since g_bundle asks me to select a group of top and a group of bottom atoms, I would need to create an index group with my first group (top) being the top residues of both my helices and the second group being the bottom residues of my helices. Or would I create Per the documentation, that sounds right. The program reads two index groups and divides both of them in -na parts. The centers of mass of these parts define the tops and bottoms of the axes. -Justin a first group for my first helix and a second group for my second helix? As I waited for the answer I ran some tests using: In a first analysis the top residues for both helices in one group and the bottom residues of both helices in another group and set the -na flag in g_bundle as 2. In a second analysis I used in my first helix a the first group and the second helix as the second group and set the -na flag as 4. Both analysis were made using alpha carbons only. I had already measured the interhelical tilt between these helices with another program called qhelix. The problem is that it gives me loads of problems with the sampling, since qhelix only measures each frame at a time and I have to convert each frame into a pdb file (etc), but anyway, it gave me interhelical tilt values that allowed me to see a trend there. When I compared the results between both methods described above, the second one gave similar results to the ones I got from qhelix. I wrote this because maybe I understood wrong your last email, the phrase Per the documentation, that sounds right. refered to the sentece above or below your statement? Thank you -- 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] Re: Re: Re: Re: g_bundle problem
Stefan Hoorman wrote: Stefan Hoorman wrote: snip I have tried using g_sgangle, but the problem is that it does not calculate the principal axis of the helix. Since g_sgangle allows me to choose at maximum 3 atoms per analysis, it is quite difficult to perform such an analysis if one is to do this for 4 or five different systems and dimers. So, in this case, since g_bundle asks me to select a group of top and a group of bottom atoms, I would need to create an index group with my first group (top) being the top residues of both my helices and the second group being the bottom residues of my helices. Or would I create Per the documentation, that sounds right. The program reads two index groups and divides both of them in -na parts. The centers of mass of these parts define the tops and bottoms of the axes. -Justin a first group for my first helix and a second group for my second helix? As I waited for the answer I ran some tests using: In a first analysis the top residues for both helices in one group and the bottom residues of both helices in another group and set the -na flag in g_bundle as 2. In a second analysis I used in my first helix a the first group and the second helix as the second group and set the -na flag as 4. Both analysis were made using alpha carbons only. I had already measured the interhelical tilt between these helices with another program called qhelix. The problem is that it gives me loads of problems with the sampling, since qhelix only measures each frame at a time and I have to convert each frame into a pdb file (etc), but anyway, it gave me interhelical tilt values that allowed me to see a trend there. When I compared the results between both methods described above, the second one gave similar results to the ones I got from qhelix. I wrote this because maybe I understood wrong your last email, the phrase Per the documentation, that sounds right. refered to the sentece above or below your statement? Thank you Sorry, my embedded comment must not have been as clear as it looked in my head :) The reference I made was to your first statement. As worded, it appears that groups with residues defining top and bottom should be created, not differently helices independently. If that does not gel with reality, then maybe the wording of the documentation is not quite right; otherwise you'll have to look into the code to see how it's doing the calculations. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Re: cutoff problem
On Mar 24, 2010, at 10:58 PM, Vitaly V. Chaban wrote: Hi, I want to test different values of cutoff for vdw. However, in the list someone said cutoff = 0.9 for vdw was used for paramaterizing of Gromos force field, other values would cause error, and also there was someone saying that cutoff for vdw should be set to 1.4. Can someone make this question clear? Thanks a lot. The common rule for all FFs is to set the LJ-cutoff around 2.5*sigma(LJ12-6). In fact, you'll get about 0.9 nm for the most objects. I see nothing terrible if you use, say, 1.4 nm just because the difference will be negligible. Where is that coming from? This is so wrong! Just test it. :) I've you ever tried that on a lipid bilayer? Who could ever say (whatever force field) a vdW cutoff of 0.9/1.4 nm is no difference? -- Dr. Vitaly Chaban -- 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 -- 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
[gmx-users] CG Force and Potential through do_force()
Hi I want to do Coarse-Grained simulation in Gromacs. I have one CG force formula, which I plan to implement by adding a short code in do_force() routine in Gromacs 4.0.7 source code. After browsing through the do_force() code, I am now familiar with data structure relevant to add the new force. I mean, I can specify new force by adding to f[indx][XX] and so on. But I am not very sure about potential, whether do I have to explicitly specify the potential on atoms due to this force or gromacs automatically takes care of it by knowing the forces on each atoms? thanks sikandar -- 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
[gmx-users] Hydrogen Bond Acceptor-Donor List
Hi ALL, Is there any way in GROMACS to get the residue list (acceptor-donor list) for an entire simulation? Using g_hbond we get the number of h-bonds at every frames. But I want to get the list of residue pairs forming those hbonds at every frame. Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- 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] CG Force and Potential through do_force()
well if I need to add it by myself, I am not very sure in what variable to add it to. Like I said, I know to add the force on the atom i do f[indxofatom][XX]= forcevalue, where to potential value due to this force? thanks sikandar On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 25/03/2010 2:42 PM, Sikandar Mashayak wrote: Hi I want to do Coarse-Grained simulation in Gromacs. I have one CG force formula, which I plan to implement by adding a short code in do_force() routine in Gromacs 4.0.7 source code. After browsing through the do_force() code, I am now familiar with data structure relevant to add the new force. I mean, I can specify new force by adding to f[indx][XX] and so on. But I am not very sure about potential, whether do I have to explicitly specify the potential on atoms due to this force or gromacs automatically takes care of it by knowing the forces on each atoms? You will need to add that yourself if you want the reported potential to be accurate. GROMACS uses the given parameters in its inner loops to calculate energies and forces. The former are not reverse-engineered from the latter. If the potential is never used, however, then you can forget about it... Mark -- 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 -- 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
