Re: [gmx-users] Why density increase with increasing the cutoff length?
On 12/21/09 8:55 AM, XAvier Periole wrote: Would it be all cut-offs: elect + vdW ? Or the increase is separate? For your info the vdW are attractive potentials at long distances so an increase of cutoff would result in an increase of attraction and therefore to an increase of density! This is one good illustration of the fact that you should not change the cutoff values from the ones used for the parameterization of a force field. In general I agree, however for some popular force fields like OPLS this is not so well-defined. Jorgensen uses different cut-offs in different papers. Using PME and dispersion correction means you are almost independent of the cut-off length (if they are not too short). Typically 1 nm and upwards will give you the same results with these settings. If you're using plain cut-offs or RF you're on your own. On Dec 21, 2009, at 8:03 AM, Yanmei Song wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- 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] Why density increase with increasing the cutoff length?
From what my Professor told me it is my understanding that cutoff length is somewhat a trade-off between accuracy of the simulation and length of time to generate the simulation. A higher cut-off indicates more accuracy but will take longer to simulate. I use low cut-offs for less important simulations like energy minimizations. An increase in density would mean a larger number of simulated molecules and therefore a need for a higher cut-off for more accurate data. That is my best theory anyway. Arden Perkins On Sun, Dec 20, 2009 at 11:03 PM, Yanmei Song yson...@asu.edu wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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
Re: [gmx-users] multiple eigenvectors with -linfix and the application of eigenvalues
Hi Chris, the eigenvalues (-eig) are only read/used in case of flooding. The behaviour for each eigenvector is solely controlled by its reference (initial) projection, and the step size. Carsten On Dec 19, 2009, at 5:16 PM, chris.ne...@utoronto.ca wrote: Hello, When utilizing more than one eigenvector in make_edi -linfix, are the eigenvector linearly combined with their eigenvalues as coefficients, or does this combination occur in the absence of eigenvalues? Thank you, Chris. -- 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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 obtain corresponding conformation for each point in the 2-D projection
Ni hao, Since it's a projection, there is not (in general) a single conformation for each point in the 2D plane. On the other hand, the points you obtained are derived from distinct (ordered) conformations, so it is trivial to retrieve them. Each conformation (time) yields one point: find the time for which the point corresponds with the one your interested in, and extract the conformation from the trajectory. Cheers, Tsjerk 2009/12/20 xi zhao zhaoxiitc2...@yahoo.com.cn Dear users for gromacs: We know that observing the sampled conformations in the subspace spanned by the eigenvectors is a so-called two-dimensional projection(2D projection), in 2-D projection, each point represents a snapshot from the simulation, and the distribution shows the sampled region along the first two eigenvectors during the simulation. But I feel confounded, because I do not know to how to obtain corresponding conformation for each point in the 2-D projection.Please help me! best regards! thank you! [image: 4]http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 -- 好玩贺卡等你发，邮箱贺卡全新上线！http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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] Why density increase with increasing the cutoff length?
From what my Professor told me it is my understanding that cutoff length is somewhat a trade-off between accuracy of the simulation and length of time to generate the simulation. A higher cut-off indicates more accuracy but will take longer to simulate. I use low cut-offs for less important simulations like energy minimizations. An increase in density would mean a larger number of simulated molecules and therefore a need for a higher cut-off for more accurate data. That is my best theory anyway. This point of view implies that the potentials used are perfect and then indeed the longer cutoff you use the more accurate your interactions energies become. You have to consider that current potential are parameterized to reproduce some data (structural and thermodynamics experimental data) and this using a given cutoff. Modifying the cutoff means that you modify the potential and therefore the model will not necessarily (and most often) fit the experimental data anymore. Arden Perkins On Sun, Dec 20, 2009 at 11:03 PM, Yanmei Song yson...@asu.edu wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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 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] Why density increase with increasing the cutoff length?
Arden Perkins wrote: From what my Professor told me it is my understanding that cutoff length is somewhat a trade-off between accuracy of the simulation and length of time to generate the simulation. A higher cut-off indicates more accuracy but will take longer to simulate. I use low cut-offs for less important simulations like energy minimizations. A higher cut-off does not necessarily indicate higher accuracy, for the parameterization process used a particular cut-off. The model physics is defined by all of the functional form, parameters, cut-offs, etc. The validity of the parameters is intrinsically linked to that cut-off. One might be able to demonstrate that one can get equivalently valid results with a different (i.e. longer) cut-off, but then there's not yet a demonstrated *increase* in accuracy. If the same parameters can produce a better model physics at a longer cut-off, then there's probably a case for further parameterization to do equivalently well for lower cost. All this assumes a non-Ewald method. PME is a different matter entirely. An increase in density would mean a larger number of simulated molecules and therefore a need for a higher cut-off for more accurate data. That is my best theory anyway. A higher density for a given cut-off increases the number of interaction partners for each atom, but that implies nothing about the accuracy of the model of that system at that density. A move from one density to another during equilibration at a given cut-off tends to indicate the unsuitability of the model physics at the former density. Xavier Periole: But I think we all agree on these issues: the treatment of long-range interactions are delicate :)) Agreed, treating long-range interactions is delicate :-) Mark On Sun, Dec 20, 2009 at 11:03 PM, Yanmei Song yson...@asu.edu mailto:yson...@asu.edu wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto: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 obtain corresponding conformation for each point in the 2-D projection
Dear Mr Tsjerk Wassenaar ： Thank you for your help! what you said is reasonal, but how to implement them, or detial procedure? The 2d projections can convert to a free energy landscape, and how to obtain conformation in the minimum of energy surface? best regards! --- 09年12月21日，周一, Tsjerk Wassenaar tsje...@gmail.com 写道： 发件人: Tsjerk Wassenaar tsje...@gmail.com 主题: Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2009年12月21日,周一,下午7:57 Ni hao, Since it's a projection, there is not (in general) a single conformation for each point in the 2D plane. On the other hand, the points you obtained are derived from distinct (ordered) conformations, so it is trivial to retrieve them. Each conformation (time) yields one point: find the time for which the point corresponds with the one your interested in, and extract the conformation from the trajectory. Cheers, Tsjerk 2009/12/20 xi zhao zhaoxiitc2...@yahoo.com.cn Dear users for gromacs: We know that observing the sampled conformations in the subspace spanned by the eigenvectors is a so-called two-dimensional projection(2D projection), in 2-D projection, each point represents a snapshot from the simulation, and the distribution shows the sampled region along the first two eigenvectors during the simulation. But I feel confounded, because I do not know to how to obtain corresponding conformation for each point in the 2-D projection.Please help me! best regards! thank you! 好玩贺卡等你发，邮箱贺卡全新上线！ -- 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. Computational Chemist Medicinal Chemist Neuropharmacologist -下面为附件内容- -- 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 ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.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] essential dynamics mdrun with SD integrator yields segmentation fault
Hi Chris, the segfault was due to the fact that with the sd integrator the constraints have to be evaluated twice and in the second call there is no pointer to the velocities present. I have fixed that in the master and release-4-0- patches branches. The velocity correction is now only done when velocities are present. Carsten On Dec 19, 2009, at 2:09 AM, chris.ne...@utoronto.ca wrote: Hello, In my hands, mdrun throws a segfault when passing the -ei flag to mdrun and utilizing the sd integrator. I'll admit that I have only tried this with a single system. Nevertheless, using -linacc vs. -linfix makes no difference, neither does moving to constraints=none or parallel vs. serial mdrun. However, when I change sd to md, the run is fine. With sd and -ei, the segfault is immediate: $ mdrun -deffnm edi -nosum -dlb yes -npme -1 -cpt 30 -maxh 48 -cpi edi.cpt -ei testpositive.edi -eo testpositive.edo :-) G R O M A C S (-: GROup of MAchos and Cynical Suckers :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun (-: Option Filename Type Description -sedi.tpr InputRun input file: tpr tpb tpa -oedi.trr Output Full precision trajectory: trr trj cpt -xedi.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpiedi.cpt Input, Opt! Checkpoint file -cpoedi.cpt Output, Opt. Checkpoint file -cedi.gro Output Structure file: gro g96 pdb -eedi.edr Output Energy file: edr ene -gedi.log Output Log file -dgdl edi.xvg Output, Opt. xvgr/xmgr file -field edi.xvg Output, Opt. xvgr/xmgr file -table edi.xvg Input, Opt. xvgr/xmgr file -tablep edi.xvg Input, Opt. xvgr/xmgr file -tableb edi.xvg Input, Opt. xvgr/xmgr file -rerun edi.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpiedi.xvg Output, Opt. xvgr/xmgr file -tpid edi.xvg Output, Opt. xvgr/xmgr file -ei testpositive.edi Input, Opt! ED sampling input -eo testpositive.edo Output, Opt! ED sampling output -jedi.gct Input, Opt. General coupling stuff -joedi.gct Output, Opt. General coupling stuff -ffout edi.xvg Output, Opt. xvgr/xmgr file -devout edi.xvg Output, Opt. xvgr/xmgr file -runav edi.xvg Output, Opt. xvgr/xmgr file -pxedi.xvg Output, Opt. xvgr/xmgr file -pfedi.xvg Output, Opt. xvgr/xmgr file -mtxedi.mtx Output, Opt. Hessian matrix -dnedi.ndx Output, Opt. Index file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint19 Set the nicelevel -deffnm string edi Set the default filename for all file options -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -[no]pd bool no Use particle decompostion -dd vector 0 0 0 Domain decomposition grid, 0 is optimize -npmeint-1 Number of separate nodes to be used for PME, -1 is guess -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -[no]ddcheck bool yes Check for all bonded interactions with DD -rdd real 0 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates -rconreal 0 Maximum distance for P-LINCS (nm), 0 is estimate -dlb enum yes Dynamic load balancing (with DD): auto, no or yes -dds real 0.8 Minimum allowed dlb scaling of the DD cell size -[no]sum bool no Sum the energies at every step -[no]v bool no Be loud and noisy -[no]compact bool yes Write a compact log file -[no]seppot bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -pforce real -1 Print all forces larger than this (kJ/mol nm) -[no]reprod bool no Try to avoid optimizations that affect binary reproducibility -cpt
[gmx-users] calculaton of electrostatic potential
Hi all, I want to calculate the electrostatic potential of my simulated membrane system (DMPC). I think, I need to make an index file for this purpose. Isn't it? In that case, how could I make the selection, I mean i have to select the whole membrane group or I have to create an index file with some particular specific atoms? I need some idea to understand this. Could someone pls help me! Best regards, /Henry Biochemistry -- 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] multiple eigenvectors with -linfix and the application of eigenvalues
Thank you Carsten for this information and for the sd/edi fix. This actually makes a bunch of sense. I can effect the eigenvalues with -linfix -linstep, and I see now that eigenvalues can not be sensibly combined with -linacc in in its current incarnation. Thank you, Chris. -- original message -- Hi Chris, the eigenvalues (-eig) are only read/used in case of flooding. The behaviour for each eigenvector is solely controlled by its reference (initial) projection, and the step size. Carsten On Dec 19, 2009, at 5:16 PM, chris.neale at utoronto.ca wrote: Hello, When utilizing more than one eigenvector in make_edi -linfix, are the eigenvector linearly combined with their eigenvalues as coefficients, or does this combination occur in the absence of eigenvalues? Thank you, Chris. -- gmx-users mailing listgmx-users at 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 thewww interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] Why density increase with increasing the cutoff length?
Thanks for all the helpful response. But do I have to use dispersion correction when I use PME? I don't quite understand what dispersion correction do. Sometime I found using dispersion correction make my results worse for a large molecule system. On Mon, Dec 21, 2009 at 12:48 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 12/21/09 8:03 AM, Yanmei Song wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University Van der Waals interactions. I guess you have not turned on the dispersion correction. If you do the effect should be far less. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- 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 -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- 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] Why density increase with increasing the cutoff length?
On 12/21/09 5:32 PM, Yanmei Song wrote: Thanks for all the helpful response. But do I have to use dispersion correction when I use PME? I don't quite understand what dispersion correction do. Sometime I found using dispersion correction make my results worse for a large molecule system. Read the manual please. On Mon, Dec 21, 2009 at 12:48 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 12/21/09 8:03 AM, Yanmei Song wrote: Dear Users: Anyone can explain why the density of the water models increase with increase the cutoff length. I tried a couple water models in reaction-field, PME simulations.The cutoff length ranged from 0.9 to 1.5. They all show the same trend. Then there must be some reasons. Anyone can tell me why? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University Van der Waals interactions. I guess you have not turned on the dispersion correction. If you do the effect should be far less. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se sp...@gromacs.org mailto:sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- 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] editconf.
Dear Users, Re Introductory tutorial; Trying to run the following: editconf -f out.gro -o fws_ctr.gro -center x/2 y/2 z/2 I get the error message, Fatal error: Expected a real argument for option -center Can anyone help, Many Thanks, David. -- 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] editconf.
On Dec 21, 2009, at 5:26 PM, david.lisgar...@canterbury.ac.uk david.lisgar...@canterbury.ac.uk wrote: Dear Users, Re Introductory tutorial; Trying to run the following: editconf -f out.gro -o fws_ctr.gro -center x/2 y/2 z/2 You have to give real coordinates for the center, not in terms of x, y, z. The coordinates are given e.g. at the end of the gro file. Carsten -- 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 can I reconstruct the system in CGMD simulation?
Dear Justin, Thank you for your message. I have found some experimental evidence to suggest that the secondary structure information of protein how change during the reaction of the unfolding. In the other hand, I have percentage of the secondary structure information (%alpha-Helix, %beta-sheet and %Random coil) of the protein at different time of reaction. Could I perform CGMD simulation with MArtini force field for finding the denaturation mechanism of the protein properly? Best regards Rasoul On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: rasoul nasiri wrote: Dear Cesar, Thank you for your reply, There are two different kind of water gro in this site (one of them is water.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.htmland another is water-1bar-303k.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html. Is there difference between them? Maybe, but if you do sufficient equilibration, it probably won't matter. Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script? No. This has been stated before - the awk script is explicitly for protein. And besides, each W CG particle corresponds to about four water molecules, so there is no trivial way to decide how to build the CG water system from spc216.gro. Another question; How can I change secondary structure information during CGMD simulation, If I want to perform CGMD simulation for finding of the folding/unfolding mechanism in proteins completely? Because Martini CGFF consider fix it. You specify the secondary structure when building the initial topology. As you've been advised already, this fixed representation of secondary structure is going to be a major limitation of using the MARTINI force field for your simulations. How do you know that whatever alternate secondary structure you've applied is valid? If you have some experimental evidence to suggest that certain peptide regions convert between one form and another, that's fine, but how do you know that the pathway taken is not an artifact of your choice to abruptly impose a change in the topology? -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 -- 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 can I reconstruct the system in CGMD simulation?
rasoul nasiri wrote: Dear Justin, Thank you for your message. I have found some experimental evidence to suggest that the secondary structure information of protein how change during the reaction of the unfolding. In the other hand, I have percentage of the secondary structure information (%alpha-Helix, %beta-sheet and %Random coil) of the protein at different time of reaction. Could I perform CGMD simulation with MArtini force field for finding the denaturation mechanism of the protein properly? I would be extremely suspicious of any results you get. As you've been told before, secondary structure is a fixed aspect of a MARTINI CG simulation. Making changes is somewhat arbitrary and may lead to artifacts that you can't anticipate. Besides, if you only know percentages of secondary structure (from CD I assume?) then you don't really know the structures and sequences that are changing, do you? Net result: this particular CG model is probably not suitable for such a simulation. -Justin Best regards Rasoul On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: rasoul nasiri wrote: Dear Cesar, Thank you for your reply, There are two different kind of water gro in this site (one of them is water.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html and another is water-1bar-303k.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html . Is there difference between them? Maybe, but if you do sufficient equilibration, it probably won't matter. Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script? No. This has been stated before - the awk script is explicitly for protein. And besides, each W CG particle corresponds to about four water molecules, so there is no trivial way to decide how to build the CG water system from spc216.gro. Another question; How can I change secondary structure information during CGMD simulation, If I want to perform CGMD simulation for finding of the folding/unfolding mechanism in proteins completely? Because Martini CGFF consider fix it. You specify the secondary structure when building the initial topology. As you've been advised already, this fixed representation of secondary structure is going to be a major limitation of using the MARTINI force field for your simulations. How do you know that whatever alternate secondary structure you've applied is valid? If you have some experimental evidence to suggest that certain peptide regions convert between one form and another, that's fine, but how do you know that the pathway taken is not an artifact of your choice to abruptly impose a change in the topology? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto: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 can I reconstruct the system in CGMD simulation?
Hi, Thank you for your quick reply. Is there another CGFF for this purpose that Gromacs can read it? What is your opinion about CG GO model? Kind regards Rasoul On Mon, Dec 21, 2009 at 8:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: rasoul nasiri wrote: Dear Justin, Thank you for your message. I have found some experimental evidence to suggest that the secondary structure information of protein how change during the reaction of the unfolding. In the other hand, I have percentage of the secondary structure information (%alpha-Helix, %beta-sheet and %Random coil) of the protein at different time of reaction. Could I perform CGMD simulation with MArtini force field for finding the denaturation mechanism of the protein properly? I would be extremely suspicious of any results you get. As you've been told before, secondary structure is a fixed aspect of a MARTINI CG simulation. Making changes is somewhat arbitrary and may lead to artifacts that you can't anticipate. Besides, if you only know percentages of secondary structure (from CD I assume?) then you don't really know the structures and sequences that are changing, do you? Net result: this particular CG model is probably not suitable for such a simulation. -Justin Best regards Rasoul On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: rasoul nasiri wrote: Dear Cesar, Thank you for your reply, There are two different kind of water gro in this site (one of them is water.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html and another is water-1bar-303k.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html . Is there difference between them? Maybe, but if you do sufficient equilibration, it probably won't matter. Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script? No. This has been stated before - the awk script is explicitly for protein. And besides, each W CG particle corresponds to about four water molecules, so there is no trivial way to decide how to build the CG water system from spc216.gro. Another question; How can I change secondary structure information during CGMD simulation, If I want to perform CGMD simulation for finding of the folding/unfolding mechanism in proteins completely? Because Martini CGFF consider fix it. You specify the secondary structure when building the initial topology. As you've been advised already, this fixed representation of secondary structure is going to be a major limitation of using the MARTINI force field for your simulations. How do you know that whatever alternate secondary structure you've applied is valid? If you have some experimental evidence to suggest that certain peptide regions convert between one form and another, that's fine, but how do you know that the pathway taken is not an artifact of your choice to abruptly impose a change in the topology? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto: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 -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] How can I reconstruct the system in CGMD simulation?
rasoul nasiri wrote: Hi, Thank you for your quick reply. Is there another CGFF for this purpose that Gromacs can read it? What is your opinion about CG GO model? There are several CG models out there, but I don't know much about them. The nice thing about Gromacs is that it can use any force field you can find. As for Go-models, you've already been given advice on that topic: http://lists.gromacs.org/pipermail/gmx-users/2009-December/047496.html -Justin Kind regards Rasoul On Mon, Dec 21, 2009 at 8:23 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: rasoul nasiri wrote: Dear Justin, Thank you for your message. I have found some experimental evidence to suggest that the secondary structure information of protein how change during the reaction of the unfolding. In the other hand, I have percentage of the secondary structure information (%alpha-Helix, %beta-sheet and %Random coil) of the protein at different time of reaction. Could I perform CGMD simulation with MArtini force field for finding the denaturation mechanism of the protein properly? I would be extremely suspicious of any results you get. As you've been told before, secondary structure is a fixed aspect of a MARTINI CG simulation. Making changes is somewhat arbitrary and may lead to artifacts that you can't anticipate. Besides, if you only know percentages of secondary structure (from CD I assume?) then you don't really know the structures and sequences that are changing, do you? Net result: this particular CG model is probably not suitable for such a simulation. -Justin Best regards Rasoul On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: rasoul nasiri wrote: Dear Cesar, Thank you for your reply, There are two different kind of water gro in this site (one of them is water.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html and another is water-1bar-303k.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html . Is there difference between them? Maybe, but if you do sufficient equilibration, it probably won't matter. Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script? No. This has been stated before - the awk script is explicitly for protein. And besides, each W CG particle corresponds to about four water molecules, so there is no trivial way to decide how to build the CG water system from spc216.gro. Another question; How can I change secondary structure information during CGMD simulation, If I want to perform CGMD simulation for finding of the folding/unfolding mechanism in proteins completely? Because Martini CGFF consider fix it. You specify the secondary structure when building the initial topology. As you've been advised already, this fixed representation of secondary structure is going to be a major limitation of using the MARTINI force field for your simulations. How do you know that whatever alternate secondary structure you've applied is valid? If you have some experimental evidence to suggest that certain peptide regions convert between one form and another, that's fine, but how do you know that the pathway taken is not an artifact of your choice to abruptly impose a change in the topology? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please
[gmx-users] Solvent Accessible Area with different Claculation Groups
Hi, We are examining a system comprising of two molecules (called mol1 and mol2) in water that are initially separated by 1.5nm. We calculate the surface accessible area of the first molecule ( mol1) in two ways: (a) sasa_a: by setting both the output and calculation groups to mol 1 (b) sasa_b: setting the calculation group to mol1 and mol2, and output group to mol1 During the simulation, the molecules are separated by more 1.5nm and since the probe radius = 0.14nm, we expected the values of the two surface areas to be identical. Instead we found sasa_a and sasa_b to differ by about +- 1.5 nm^2. Although this variation is small compared to the mean value ~86 nm^2, it has caused us some concern. We were also surprised that sasa_b was larger than sasa_a for part of the simulation. (The same trend is observed when the accuracy of the calculation was increased by using ndots=48). I was wondering if anyone has some insight on why the two sasa values are not identical. I am attaching a figure displaying the calculations described above, obtained by: g_sas -f /traj-0-37 -s top.tpr -n index-1-2.ndx -b 0 -e 100 -ndots 24 Many thanks for your help, Loukas Loukas Petridis Post-doctoral Research Fellow Center for Molecular Biophysics, Oak Ridge National Laboratory Building 6011, MS 6309, Oak Ridge, TN 37831 865-576-2576 http://cmb.ornl.gov/people/lpk attachment: sasa.pngattachment: mindist.png-- 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] Solvent Accessible Area with different Claculation Groups
Petridis, Loukas wrote: Hi, We are examining a system comprising of two molecules (called mol1 and mol2) in water that are initially separated by 1.5nm. We calculate the surface accessible area of the first molecule ( mol1) in two ways: (a) sasa_a: by setting both the output and calculation groups to mol 1 (b) sasa_b: setting the calculation group to mol1 and mol2, and output group to mol1 During the simulation, the molecules are separated by more 1.5nm and since the probe radius = 0.14nm, we expected the values of the two surface areas to be identical. Instead we found sasa_a and sasa_b to differ by about +- 1.5 nm^2. Although this variation is small compared to the mean value ~86 nm^2, it has caused us some concern. We were also surprised that sasa_b was larger than sasa_a for part of the simulation. (The same trend is observed when the accuracy of the calculation was increased by using ndots=48). I was wondering if anyone has some insight on why the two sasa values are not identical. From g_sas -h: The calculation group should always consists of all the non-solvent atoms in the system. The output group can be the whole or part of the calculation group. So, setting the calculation group to only include mol1 is simply incorrect usage of the program. -Justin I am attaching a figure displaying the calculations described above, obtained by: g_sas -f /traj-0-37 -s top.tpr -n index-1-2.ndx -b 0 -e 100 -ndots 24 Many thanks for your help, Loukas Loukas Petridis Post-doctoral Research Fellow Center for Molecular Biophysics, Oak Ridge National Laboratory Building 6011, MS 6309, Oak Ridge, TN 37831 865-576-2576 http://cmb.ornl.gov/people/lpk -- 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] Using GENCONF
Hi all, Is there a way to use genconf such that it does not reproduce the exact same coordinates over and over again (or multiples of the same coordinates) but assigns different coordinate values to each atom in the x, y and z directions? Thanks, Lum -- 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] Using GENCONF
Lum Nforbi wrote: Hi all, Is there a way to use genconf such that it does not reproduce the exact same coordinates over and over again (or multiples of the same coordinates) but assigns different coordinate values to each atom in the x, y and z directions? Sort of. See genconf -h 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] calculaton of electrostatic potential
Henry Yang wrote: Hi all, I want to calculate the electrostatic potential of my simulated membrane system (DMPC). I think, I need to make an index file for this purpose. Isn't it? In that case, how could I make the selection, I mean i have to select the whole membrane group or I have to create an index file with some particular specific atoms? I need some idea to understand this. Could someone pls help me! Sounds like you should read g_potential -h and/or http://www.gromacs.org/Documentation/File_Formats/Index_File and then work out how to articulate clearly what it is you want to calculate. That should guide you to how to calculate 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
Re: [gmx-users] editconf.
Carsten Kutzner wrote: On Dec 21, 2009, at 5:26 PM, david.lisgar...@canterbury.ac.uk david.lisgar...@canterbury.ac.uk wrote: Dear Users, Re Introductory tutorial; Trying to run the following: editconf -f out.gro -o fws_ctr.gro -center x/2 y/2 z/2 You have to give real coordinates for the center, not in terms of x, y, z. The coordinates are given e.g. at the end of the gro file. The dimensions of the box are given at the end of the .gro file. 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] Solvent Accessible Area with different Claculation Groups
Justin A. Lemkul wrote: Petridis, Loukas wrote: Hi, We are examining a system comprising of two molecules (called mol1 and mol2) in water that are initially separated by 1.5nm. We calculate the surface accessible area of the first molecule ( mol1) in two ways: (a) sasa_a: by setting both the output and calculation groups to mol 1 (b) sasa_b: setting the calculation group to mol1 and mol2, and output group to mol1 During the simulation, the molecules are separated by more 1.5nm and since the probe radius = 0.14nm, we expected the values of the two surface areas to be identical. Instead we found sasa_a and sasa_b to differ by about +- 1.5 nm^2. Although this variation is small compared to the mean value ~86 nm^2, it has caused us some concern. We were also surprised that sasa_b was larger than sasa_a for part of the simulation. (The same trend is observed when the accuracy of the calculation was increased by using ndots=48). I was wondering if anyone has some insight on why the two sasa values are not identical. From g_sas -h: The calculation group should always consists of all the non-solvent atoms in the system. The output group can be the whole or part of the calculation group. So, setting the calculation group to only include mol1 is simply incorrect usage of the program. I'm not sure this is correct actually (although there has been a bug in the program for a long time). But if you want to e.g. compute the occluded area in a protein-protein interaction you have to compute A+B-AB where A is the area of just protein A, ignoring everything else and so on. The fact the OP does not get the same area (did he use the same molecules?) is probably just poor sampling. Just wait a couple of hundred nanoseconds and see whether the distributions overlap. -Justin I am attaching a figure displaying the calculations described above, obtained by: g_sas -f /traj-0-37 -s top.tpr -n index-1-2.ndx -b 0 -e 100 -ndots 24 Many thanks for your help, Loukas Loukas Petridis Post-doctoral Research Fellow Center for Molecular Biophysics, Oak Ridge National Laboratory Building 6011, MS 6309, Oak Ridge, TN 37831 865-576-2576 http://cmb.ornl.gov/people/lpk -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- 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
