[gmx-users] positive potential energy
Hi dear all I'm simulating a system containing CNT, when I put CNT in a unit cell and want to run energy minimization in a vacuum, I encounter with such an error: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing, after running grompp. I've tried a lot of numbers for cut-off radius ,but I didn't get any result, at last I changed the coulomb type from PME to Cut-off, and it worked, I want to know if my results will be reasonable in this case or not, and how to solve that error. thank you in advanced Bests -Zahra -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: positive potential energy
Sorry ...I forget to announce that my potential energy is positive, is it logical? From: Zahra M s_zahra_mous...@yahoo.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Thursday, December 29, 2011 12:52 PM Subject: positive potential energy Hi dear all I'm simulating a system containing CNT, when I put CNT in a unit cell and want to run energy minimization in a vacuum, I encounter with such an error: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing, after running grompp. I've tried a lot of numbers for cut-off radius ,but I didn't get any result, at last I changed the coulomb type from PME to Cut-off, and it worked, I want to know if my results will be reasonable in this case or not, and how to solve that error. thank you in advanced Bests -Zahra-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: positive potential energy
On 29/12/2011 8:24 PM, Zahra M wrote: Sorry ...I forget to announce that my potential energy is positive, is it logical? No. *From:* Zahra M s_zahra_mous...@yahoo.com *To:* gmx-users@gromacs.org gmx-users@gromacs.org *Sent:* Thursday, December 29, 2011 12:52 PM *Subject:* positive potential energy Hi dear all I'm simulating a system containing CNT, when I put CNT in a unit cell and want to run energy minimization in a vacuum, I encounter with such an error: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing, after running grompp. I've tried a lot of numbers for cut-off radius ,but I didn't get any result, at last I changed the coulomb type from PME to Cut-off, and it worked, I want to know if my results will be reasonable in this case or not, and how to solve that error. It's not an error, but an advisory about your performance, and doesn't matter for EM in vacuo which will only run for a few seconds. Using a plain cut-off is unreasonable by definition, but doesn't matter for EM in vacuo. Otherwise, you should note that the suggestion is to increase the cut-off *and* the PME grid spacing, not just one of them. Mark thank you in advanced Bests -Zahra -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Generating Pairs with a Buckingham Potential
Hi Mark, Thanks for your reply! I'm sorry, you're right, as far as I know the manual doesn't actually mention Buckingham pairs generation... but when I set gen-pairs to yes and run grompp, I get the following error: Generating pair parameters is only supported with LJ non-bonded interactions I guess I'm wondering how anyone can use the Buckingham potential at all, since Gromacs does not appear to support pairs generation for the Buckingham or the use of explicitly defined Buckingham pair parameters (when defining [ pairtypes ], you have to give the parameters in LJ form). Thanks so much again, Olivia On Wed, Dec 28, 2011 at 8:28 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/12/11, *Olivia Waring *owar...@princeton.edu wrote: I apologize for the truncated message; I pressed send too soon. According to the Gromacs manual, pairs cannot be generated automatically for the Buckingham potential, Where does it say this? but the [ pairtypes ] directive seems to only accept parameters in LJ form (i.e. c6 and c12, instead of a, b, and c6). I've been looking into ways to interconvert between the two potential forms, but haven't found anything... Can anyone who has successfully generated a topology using the Buckingham potential shed light on this issue? You want a 1-4 interaction using Buckingham functional form? If so, I don't think GROMACS supports it. If you're trying to combine bits of force fields that use L-J with bits of force fields that use Buckingham, then that's almost certainly a bad idea. Mark Thank you so much, Olivia On Wed, Dec 28, 2011 at 11:05 AM, Olivia Waring owar...@princeton.eduwrote: Hello Gromacs users, I'm using a Buckingham potential for the nonbonded interactions in my system, so I have the following lines in my forcefield.itp file: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no 1.0 1.0 -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_analyze -ee
Dear gromacs users I want to calculate error estimates using block averaging for output from g-dist (distance between donor atom of protein and acceptor atom of dna). I used g_analyze -f dist.xvg -ee there are 3 columns in output file. anyone give me more explain about these columns? how to explicate and interpret these data? In the one of the my output files, I encountered Read 1 sets of 1252 points, dt = 0.0119951 std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 7.918456e+00 2.788148e+00 7.882919e-02 -0.717 -0.202 Back Off! I just backed up e11grey.xvg to ./#e11grey.xvg.2# Warning: tau2 is longer than the length of the data (15.0059) the statistics might be bad invalid fit: e.e. nan a 2.07331 tau1 3.99138 tau2 183052 Will fix tau2 at the total time: 15.0059 a fitted parameter is negative invalid fit: e.e. nan a 16.5523 tau1 10.8852 tau2 15.0059 Will use a single exponential fit for set 1 Set 1: err.est. 1.26673 a 1 tau1 1.54994 tau2 0 how to fix that? Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] shell molecular dynamics
Hello, I would like to run a simulation using the shell option. I tried to restraint solvent molecules which were found within the range of 5-10 angstroms from the box center. I couldn't find any way to do so. I didn't find any information about this topic anywhere else i.e. GROMACS manual, online tutorials etc. Can anybody help me with this problem or guide me to appropriate tutorial. Thanks in advance. Michael -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] shell molecular dynamics
On 29/12/2011 9:43 PM, michael zhenin wrote: Hello, I would like to run a simulation using the shell option. I tried to restraint solvent molecules which were found within the range of 5-10 angstroms from the box center. I couldn't find any way to do so. I didn't find any information about this topic anywhere else i.e. GROMACS manual, online tutorials etc. There are some threads in the mailing list archives. You need to make two different moleculetypes, one which is position restrained, and one that isn't. Then you need to identify the ones you want to restrain, e.g. with an index group made by g_select. Then you'll need to do some cut-and-paste to get the block of restrained solvent contiguous. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to obtain error bar for plotting?
Hey :) Just some side notes. Make sure to distinguish between 'statistical error' or 'standard error of the mean', which is a measure of how 'correct' your estimate of the average is, and the standard deviation or the variance, which is a measure of the natural spread. The latter is not an error! In addition, there are correlations that make it difficult to assess the standard error of the mean. These correlations can be time correlations, which cause a false decrease of the standard error. But simulations that start from similar starting points are also correlated. If the simulations are too short, and 1 ns seems quite short, then the observations will not be statistically independent, and the standard error will again turn out smaller than it should. Cheers, Tsjerk On Thu, Dec 29, 2011 at 2:39 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 28/12/11, leila karami karami.lei...@gmail.com wrote: Dear Mark can I obtain error bar twice the standard error of the average If you've used g_energy -av on multiple sets of data, then it will plot error bars corresponding to various quantities. Since twice the standard error isn't an option it supports (as you know from reading g_energy -h) then you'll have the option of accepting one it does support or looking at the output file with error bars of (say) one standard error and post-processing to double the size. distance between the donor atom of protein and acceptor atom of dna over 1 simulation? You've made one observation from one simulation, so there is no statistical error to report. should I do several simulation. Is 1 simulation enough? Very likely you should do several simulations each much longer than 1ns. You should also examine the literature for people who've tried to observe similar things on similar systems to use their approach as a guide for your own. Mark -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 92, Issue 138
From: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Thursday, December 29, 2011 1:05 PM Subject: gmx-users Digest, Vol 92, Issue 138 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: -pbc nojump (mohammad agha) 2. positive potential energy (Zahra M) 3. Re: positive potential energy (Zahra M) 4. Re: Re: positive potential energy (Mark Abraham) -- Message: 1 Date: Wed, 28 Dec 2011 18:54:54 -0800 (PST) From: mohammad agha mra...@yahoo.com Subject: Re: [gmx-users] -pbc nojump To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 1325127294.34356.yahoomail...@web125705.mail.ne1.yahoo.com Content-Type: text/plain; charset=us-ascii Thank you very much from your reply. Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 29, 2011 1:56 AM Subject: Re: [gmx-users] -pbc nojump Hi Sara, Please keep discussions on the list. I'm not your private tutor. Whether you can do your analysis depends on the analysis you want to do. But if your aim is analyzing the formation of the micelle, you're probably better of reversing the trajectory. 1- trjconv -f md.trr -o md1.xtc -n index.ndx -pbc whole -s md.tpr This makes molecules whole, which is fine. Clustering should make molecules whole too, though, making this step redundant. 2- trjconv -f md1.xtc -s md.tpr -o cluster1.gro -e 60 -pbc cluster Fine, you get a cluster 3- trjconv -f cluster1.gro -s md.tpr -dump 150 -o cluster2.gro This does nothing special. Just because you have a reference clustered doesn't mean the output frame will turn out clustered. 4- grompp -f md.mdp -c cluster2.gro -o cluster1.tpr -n index.ndx 5- trjconv -f cluster1.gro -o cluster1.xtc -s cluster1.tpr -pbc nojump This screws up everything. You can only use -pbc nojump with a reference structure that is sufficiently close to the first frame of the trajectory. Your reference is a snapshot at t=600 ns. 6- trjconv -f cluster1.xtc -s cluster1.tpr -pbc mol -ur compact -center -o cluster3.xtc This would probably be fine if the trajectory was okay there. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20111228/d0b386d6/attachment-0001.html -- Message: 2 Date: Thu, 29 Dec 2011 01:22:15 -0800 (PST) From: Zahra M s_zahra_mous...@yahoo.com Subject: [gmx-users] positive potential energy To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 1325150535.62665.yahoomail...@web161705.mail.bf1.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi dear all I'm simulating a system containing CNT, when I put CNT in a unit cell and want to run energy minimization in a vacuum, I encounter with such an error: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing, after running grompp. I've tried a lot of numbers for cut-off radius ,but I didn't get any result, at last I changed the coulomb type from PME to Cut-off, and it worked, I want to know if my results will be reasonable in this case or not, and how to solve that error. thank you in advanced Bests -Zahra -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20111229/d842ec1a/attachment-0001.html -- Message: 3 Date: Thu, 29 Dec 2011 01:24:14 -0800 (PST) From: Zahra M s_zahra_mous...@yahoo.com Subject: [gmx-users] Re: positive potential energy To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 1325150654.64323.yahoomail...@web161705.mail.bf1.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Sorry ...I forget to announce that my potential energy is positive, is it logical? From: Zahra M s_zahra_mous...@yahoo.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Thursday, December
[gmx-users] what is a central structure
Hello everyone, I am using g_cluster with gromos method to do some clustering, and by default, -cl writes the central structure of each cluster obtained. So I wonder what 'central structure' mean? Assuming that I cluster based on RMSD values relative to the starting conformation, and that I then get a cluster with 3 structures (RMSD = 0.1, 0.2, 0.3 nm, respectively), should the structure with RMSD = 0.2 nm be the central structure? What if there are 4 structures in this cluster, with RMSD = 0.1, 0.2, 0.3, 0.4 nm, respectively? Thanks for any explanation, Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] what is a central structure
On 30/12/2011 7:49 AM, Yun Shi wrote: Hello everyone, I am using g_cluster with gromos method to do some clustering, and by default, -cl writes the central structure of each cluster obtained. So I wonder what 'central structure' mean? Assuming that I cluster based on RMSD values relative to the starting conformation, With GROMACS, you can only cluster based on the matrix of inter-structure RMSD. Clustering based on the RMSD from some reference structure provides a nearly useless measure of similarity of two structures that each have the same RMSD to that reference structure, and that measure of similarity is needed to determine cluster membership. and that I then get a cluster with 3 structures (RMSD = 0.1, 0.2, 0.3 nm, respectively), should the structure with RMSD = 0.2 nm be the central structure? What if there are 4 structures in this cluster, with RMSD = 0.1, 0.2, 0.3, 0.4 nm, respectively? The center of the cluster is the member of the structure with the smallest average RMSD to all other members of the structures. I have updated the documentation to include this. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Generating Pairs with a Buckingham Potential
On 30/12/2011 5:30 AM, Olivia Waring wrote: Hi Mark, Thanks for your reply! I'm sorry, you're right, as far as I know the manual doesn't actually mention Buckingham pairs generation... but when I set gen-pairs to yes and run grompp, I get the following error: Generating pair parameters is only supported with LJ non-bonded interactions I guess I'm wondering how anyone can use the Buckingham potential at all, since Gromacs does not appear to support pairs generation for the Buckingham or the use of explicitly defined Buckingham pair parameters (when defining [ pairtypes ], you have to give the parameters in LJ form). Why do you need pairs with your model? Mark Thanks so much again, Olivia On Wed, Dec 28, 2011 at 8:28 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 29/12/11, *Olivia Waring *owar...@princeton.edu mailto:owar...@princeton.edu wrote: I apologize for the truncated message; I pressed send too soon. According to the Gromacs manual, pairs cannot be generated automatically for the Buckingham potential, Where does it say this? but the [ pairtypes ] directive seems to only accept parameters in LJ form (i.e. c6 and c12, instead of a, b, and c6). I've been looking into ways to interconvert between the two potential forms, but haven't found anything... Can anyone who has successfully generated a topology using the Buckingham potential shed light on this issue? You want a 1-4 interaction using Buckingham functional form? If so, I don't think GROMACS supports it. If you're trying to combine bits of force fields that use L-J with bits of force fields that use Buckingham, then that's almost certainly a bad idea. Mark Thank you so much, Olivia On Wed, Dec 28, 2011 at 11:05 AM, Olivia Waring owar...@princeton.edu mailto:owar...@princeton.edu wrote: Hello Gromacs users, I'm using a Buckingham potential for the nonbonded interactions in my system, so I have the following lines in my forcefield.itp file: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no 1.0 1.0 -- Olivia Waring (???) Princeton University '12 AB Chemistry -- Olivia Waring (???) Princeton University '12 AB Chemistry -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_analyze -ee
On 30/12/2011 1:06 AM, leila karami wrote: Dear gromacs users I want to calculate error estimates using block averaging for output from g-dist (distance between donor atom of protein and acceptor atom of dna). I used g_analyze -f dist.xvg -ee there are 3 columns in output file. anyone give me more explain about these columns? Have you read g_analyze -h and perhaps consulted the reference you can find there? Mark how to explicate and interpret these data? In the one of the my output files, I encountered Read 1 sets of 1252 points, dt = 0.0119951 std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 7.918456e+00 2.788148e+00 7.882919e-02 -0.717 -0.202 Back Off! I just backed up e11grey.xvg to ./#e11grey.xvg.2# Warning: tau2 is longer than the length of the data (15.0059) the statistics might be bad invalid fit: e.e. nan a 2.07331 tau1 3.99138 tau2 183052 Will fix tau2 at the total time: 15.0059 a fitted parameter is negative invalid fit: e.e. nan a 16.5523 tau1 10.8852 tau2 15.0059 Will use a single exponential fit for set 1 Set 1: err.est. 1.26673 a 1 tau1 1.54994 tau2 0 how to fix that? Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
