Re: [gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION
Hi, You can try swissparam online tool to generate protein and ligand topologies.. Cheers, Nitin On Wed, Nov 16, 2011 at 7:03 AM, arun kumar arunjones.kuma...@gmail.comwrote: hi justin, as u said i understand that there is inconsistency in the charges and charge groups of PRODRG server itself. can u suggest me any other softwares that i can rely on for this work. Thanking you. On Tue, Nov 15, 2011 at 7:48 PM, gmx-users-requ...@gromacs.org wrote: 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: ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION (Justin A. Lemkul) 2. RMSD (shahid nayeem) 3. Problem during GROMACS 4.5.5 installation (sai nitin) 4. Re: Problem during GROMACS 4.5.5 installation (Justin A. Lemkul) 5. Re: RMSD (Gianluca Santoni) 6. Re: RMSD (felmer...@uchile.cl) 7. Re: Positive potential energy for TFE solvent (Harpreet Basra) -- Message: 1 Date: Tue, 15 Nov 2011 06:40:31 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ec24faf.5050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed arun kumar wrote: Dear friends, i had a problem while running the of protein-ligand complex simulation, in which i have generated the ligand toplogy by using online Prodrg server and iam using gromos 96.1froce field. there was an note and an error during minimization NOTE 2 [file trp.top]: The largest charge group contains 15 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Analysing residue names: There are: 223Protein residues There are: 1 Other residues There are: 25853 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 161838.00 Largest charge group radii for Van der Waals: 0.790, 0.356 nm Largest charge group radii for Coulomb: 0.790, 0.399 nm WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (1.188798) is larger than rlist (1.00) i am using the mdp file the one that i copied from gromacs protein-ligand tutorial can any one please explain these errors so that i can go farward in my work. http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb and i have a doubt, as there are other updated forcefields, how much reliable is the gromos 96 ff The problem is not the reliability of Gromos96, but the reliability of PRODRG. Please read the paper linked from http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips to understand why you should almost certainly never use the charges and charge groups that PRODRG creates. -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 -- Message: 2 Date: Tue, 15 Nov 2011 17:53:19 +0530 From: shahid nayeem msnay...@gmail.com Subject: [gmx-users] RMSD To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAB_3DJa8m-jooJb= cmscmrds8ja-rzdm7gmdm+oku7s7qem...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Dear all I am interested to get contour plot of residue RMSD vs time graph. I want to get the flexible and rigid regions of protein chain during simulation. g_rmsf does not gives me this plot. Please help shahid Nayeem -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/2015/c99194fb/attachment-0001.html -- Message: 3 Date: Tue, 15 Nov 2011 14:03:03 +0100 From: sai nitin sainit...@gmail.com Subject: [gmx-users]
Re: [gmx-users] RMSD
Thanks. But in timeline plugin of VMD I am able to measure RMSD with respect to one of the frame of trajectory and I am interested to measure RMSD with respect to another molecule. I am trying to measure RMSD of trajectory frames with respect to Bound and unbound configuration of molecule so that I can compare side chain configuration of trajectory with bound and unbound sidechain configuration. Please help. Shahid Nayeem On Tue, Nov 15, 2011 at 7:02 PM, felmer...@uchile.cl felmer...@uchile.clwrote: In any case, if you really want to see flexibility then you need RMSF and not RMSD as the later will only tell you about how similar is the configuration of a sidechain compared to a reference frame. If that is still what you want i think VMD has a tool for that in the timeline plugin. regards Felipe Mensaje original De: gianluca.sant...@ibs.fr Fecha: 15-nov-2011 10:18 Para: Discussion list for GROMACS usersgmx-users@gromacs.org Asunto: Re: [gmx-users] RMSD On 11/15/11 8:23 PM, shahid nayeem wrote: Dear all I am interested to get contour plot of residue RMSD vs time graph. I want to get the flexible and rigid regions of protein chain during simulation. g_rmsf does not gives me this plot. Please help shahid Nayeem Try g_rmsf -res , it could be useful, maybe. -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- 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
Re: [gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION
Hi arun, You can try swissparam online tool to generate protein and ligand topologies.. Cheers, Nitin -- Sainitin D PhD student Bioinformatics Group Biotechnology Center Technische Universität Dresden Tatzberg 47/49 01307 Dresden, Germany Tel Lab:+49 (0)351 463 40060 -- 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] Umbrella Sampling - Justin tutorial
Hi GMX Users, I am doing Justin tutorial of Umbrella sampling. I have just finished continous pulling of chainA from the reference chainB. I have some questions. I looked at the trajectory of pulling and it has began with dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. My question is why? As you apply pulling with the constant force to the COM of the whole chain why does it start with terminal residue following then one by one? Why not the middle one or any other? The second thing I would like to extract starting configurations from from my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense as the ChainA is still within ChainB. I would like to use configurations: 0 - 0.50 50 - 0.52 100 - 0.51 150 - 0.51 200 - 0.62 250 - 2.21 500 - 5.48 My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or this configuration above is ok? Can the spacing in nm vary? And the last thing - is it required to use frames till 189 as the COM varies in this area? Thank you! Steven -- 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] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION
Please do not include the entire digest in your post. The archive becomes hopelessly confusing when this happens... arun kumar wrote: hi justin, as u said i understand that there is inconsistency in the charges and charge groups of PRODRG server itself. can u suggest me any other softwares that i can rely on for this work. Yes, ATB is one option, or you can modify the PRODRG topology after doing your own charge calculations, as described in http://pubs.acs.org/doi/abs/10.1021/ci100335w. -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/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] Pressure change after NPT equilibriation
shilpa yadahalli wrote: Dear Justin, sorry to trouble you again. I want to ask one more thing. I saw some of the documentation regarding, and i found that (on d page u mentioned frm gromacs), for a box of 216 waters, fluctuations of 500-600 bar are standard. And for a system of 21600 water molecules ~ fluctuations of 50-60 bar. My system has ~ 5000 to 6000 water molecules. So i should expect pressure fluctuations less than 500-600 bar (?). If i go acc. to above calculations then i should expect, 600 bar / (28)^1/2 = ~ 113.38 bar. [6000/216 water molecules ~ 27.78 ]. (my run time for npt equlibriation is 600 ps.) Per the page quoted before, pressure decreases as the root of the number of particles, not the square of the number of the ratio of molecules :) You should note that, if I recall, the quoted statistics are for the Berendsen barostat (a weak coupling algorithm with exponential decay) for a box of pure water. The Parrinello-Rahman barostat will have larger fluctuations. -Justin Can you pls explain me regarding. Thanks alot, Shilpa *From:* Justin A. Lemkul jalem...@vt.edu *To:* shilpa yadahalli shilpa_09ho...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, November 16, 2011 12:02 AM *Subject:* Re: [gmx-users] Pressure change after NPT equilibriation shilpa yadahalli wrote: After doing NPT simulation I plot pressure and density. How much pressure change is considered as normal? I'm getting pressure change +/- 500 bar, after doing NPT equilibration for most of my proteins. And for one of the protein it is as high as +/- 1000 bar. Can anybody tell me what is the Normal/expected pressure change. My temperature is constant 300 K. (I m running simulations at normal conditions of temperature and pressure. 300K, 1 bar, using _AMBER99SB_ FF, protein is globular with 92 amino acids). Log file etc, does not shows any warnings and simulation also does not show any inconsistent topology shifts. After my production run also, i do not get any warnings. and my rmsd is below 0.2. but i am not much happy with the pressure changing so much. Sounds completely normal. http://www.gromacs.org/Documentation/Terminology/Pressure You haven't shown your .mdp settings so it's hard to gauge what you should expect, but again, this is expected behavior for the reasons described at the above link. -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 -- 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/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] pulling force vs free energy
Hi, What is the relation between pulling force and free energy of binding. can we relate the maximum pulling force with the free energy. for example, 2 systems has the maximum pulling force and free energy as below from umbrella sampling and g_wham analysis, max. forcefree energy system 1 147042 system 2 164732 system 2 has higher pulling force than system 1 and the free energy result is different from this trend. Regards, Vijay. -- 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] pulling force vs free energy
Vijayaraj wrote: Hi, What is the relation between pulling force and free energy of binding. can we relate the maximum pulling force with the free energy. for example, 2 systems has the maximum pulling force and free energy as below from umbrella sampling and g_wham analysis, max. forcefree energy system 1 147042 system 2 164732 system 2 has higher pulling force than system 1 and the free energy result is different from this trend. How did you obtain the maximum force, just a single SMD trajectory? If so, I wouldn't put a lot of faith in it necessarily. Umbrella sampling is a more robust method than a single pull. You can use large numbers of pulling simulations and apply Jarzynski's equation to calculate free energy, but there are distinct caveats (although I suppose there are caveats with any method). -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/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] Umbrella Sampling - Justin tutorial
Steven Neumann wrote: Hi GMX Users, I am doing Justin tutorial of Umbrella sampling. I have just finished continous pulling of chainA from the reference chainB. I have some questions. I looked at the trajectory of pulling and it has began with dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. My question is why? As you apply pulling with the constant force to the COM of the whole chain why does it start with terminal residue following then one by one? Why not the middle one or any other? By pulling on the COM of any molecule, the forces are then redistributed to the other atoms. In the case given in the tutorial, the region you see dissociate first is held together by relatively weak interactions. If you pull directly on a specific residue or atom, that residue will dissociate first in all likelihood. For further discussion pertinent to this specific system, please refer to our paper linked from the tutorial. You're observing what we observed, so there is no problem and I am happy that the behavior is reproducible for others :) The second thing I would like to extract starting configurations from from my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense as the ChainA is still within ChainB. I would like to use configurations: 0 - 0.50 50 - 0.52 100 - 0.51 150 - 0.51 200 - 0.62 250 - 2.21 500 - 5.48 My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or this configuration above is ok? Can the spacing in nm vary? I'm not clear on what you mean here. In constructing a reaction coordinate, you need to sample at finite intervals along the given path. 0.2 nm is a common spacing used for many systems, and if you want to reproduce the tutorial's results, you should use that spacing. Otherwise, I can't guarantee what you will see. The peptide chains remain bound for a long time, until the force applied by the harmonic spring overcomes the intermolecular interactions. This was useful in our study (again, see the paper for why). And the last thing - is it required to use frames till 189 as the COM varies in this area? You only need one to represent the center of that particular window, since the COM distance isn't changing much here. -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/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] Umbrella Sampling - Justin tutorial
Thank you Justin, now I get what you mean! As I understood I should pick just one frame untill 189 ps (when dissociation occured) - does it matter which one I will choose on the final binding free energy? Then spacing should be 0.2 nm. Right? But how is it possible to do spacing like this from such results of summary_distances.dat: 189 0.5769072 190 0.5753590 191 0.5711223 192 0.5719844 193 0.5856807 194 0.5886649 195 0.5958101 ... 211 0.7111782 212 0.7322708 213 0.7675126 ... 378 4.2101626 379 4.1993918 380 4.2223649 .. 500 5.48839 Do you mean the approximate valueof 0.2 nm spacing? As it would be difficult with these numbers. Can you e.g. do spacing of app. 0.1 nm until e.g. 3 nm and then increase it to 0.2 nm (I think as in your paper) until 5nm? Thank you, Steven On Wed, Nov 16, 2011 at 2:31 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Hi GMX Users, I am doing Justin tutorial of Umbrella sampling. I have just finished continous pulling of chainA from the reference chainB. I have some questions. I looked at the trajectory of pulling and it has began with dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. My question is why? As you apply pulling with the constant force to the COM of the whole chain why does it start with terminal residue following then one by one? Why not the middle one or any other? By pulling on the COM of any molecule, the forces are then redistributed to the other atoms. In the case given in the tutorial, the region you see dissociate first is held together by relatively weak interactions. If you pull directly on a specific residue or atom, that residue will dissociate first in all likelihood. For further discussion pertinent to this specific system, please refer to our paper linked from the tutorial. You're observing what we observed, so there is no problem and I am happy that the behavior is reproducible for others :) The second thing I would like to extract starting configurations from from my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense as the ChainA is still within ChainB. I would like to use configurations: 0 - 0.50 50 - 0.52 100 - 0.51 150 - 0.51 200 - 0.62 250 - 2.21 500 - 5.48 My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or this configuration above is ok? Can the spacing in nm vary? I'm not clear on what you mean here. In constructing a reaction coordinate, you need to sample at finite intervals along the given path. 0.2 nm is a common spacing used for many systems, and if you want to reproduce the tutorial's results, you should use that spacing. Otherwise, I can't guarantee what you will see. The peptide chains remain bound for a long time, until the force applied by the harmonic spring overcomes the intermolecular interactions. This was useful in our study (again, see the paper for why). And the last thing - is it required to use frames till 189 as the COM varies in this area? You only need one to represent the center of that particular window, since the COM distance isn't changing much here. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Umbrella Sampling - Justin tutorial
Steven Neumann wrote: Thank you Justin, now I get what you mean! As I understood I should pick just one frame untill 189 ps (when dissociation occured) - does it matter which one I will choose on the final binding free energy? The free energy minimum should (theoretically) be when the peptides are still interacting, i.e. at time zero. Use this frame and base the spacing off of it. Then spacing should be 0.2 nm. Right? But how is it possible to do spacing like this from such results of summary_distances.dat: 189 0.5769072 190 0.5753590 191 0.5711223 192 0.5719844 193 0.5856807 194 0.5886649 195 0.5958101 ... 211 0.7111782 212 0.7322708 213 0.7675126 ... 378 4.2101626 379 4.1993918 380 4.2223649 .. 500 5.48839 Do you mean the approximate valueof 0.2 nm spacing? As it would be difficult with these numbers. Can you e.g. do spacing of app. 0.1 nm until e.g. 3 nm and then increase it to 0.2 nm (I think as in your paper) until 5nm? Choose approximate values. My protocol of uneven spacing was necessary to refine the energy minimum for the suitable data for the paper. I kept the tutorial simple; you should still achieve a reasonable result. Uneven spacing is uncommon in the literature, so I did not want to give anyone the impression that it was a standard protocol, leaving it as an exercise for the reader to understand the paper and the motivation for uneven spacing. -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/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] Umbrella Sampling - Justin tutorial
Thank you Justin! That helped a lot! Steven On Wed, Nov 16, 2011 at 3:06 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Thank you Justin, now I get what you mean! As I understood I should pick just one frame untill 189 ps (when dissociation occured) - does it matter which one I will choose on the final binding free energy? The free energy minimum should (theoretically) be when the peptides are still interacting, i.e. at time zero. Use this frame and base the spacing off of it. Then spacing should be 0.2 nm. Right? But how is it possible to do spacing like this from such results of summary_distances.dat: 189 0.5769072 190 0.5753590 191 0.5711223 192 0.5719844 193 0.5856807 194 0.5886649 195 0.5958101 ... 211 0.7111782 212 0.7322708 213 0.7675126 ... 378 4.2101626 379 4.1993918 380 4.2223649 .. 500 5.48839 Do you mean the approximate valueof 0.2 nm spacing? As it would be difficult with these numbers. Can you e.g. do spacing of app. 0.1 nm until e.g. 3 nm and then increase it to 0.2 nm (I think as in your paper) until 5nm? Choose approximate values. My protocol of uneven spacing was necessary to refine the energy minimum for the suitable data for the paper. I kept the tutorial simple; you should still achieve a reasonable result. Uneven spacing is uncommon in the literature, so I did not want to give anyone the impression that it was a standard protocol, leaving it as an exercise for the reader to understand the paper and the motivation for uneven spacing. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] pulling force vs free energy
Message: 4 Date: Wed, 16 Nov 2011 09:34:02 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pulling force vs free energy To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ec3c9da.7040...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Vijayaraj wrote: Hi, What is the relation between pulling force and free energy of binding. can we relate the maximum pulling force with the free energy. for example, 2 systems has the maximum pulling force and free energy as below from umbrella sampling and g_wham analysis, max. forcefree energy system 1 147042 system 2 164732 system 2 has higher pulling force than system 1 and the free energy result is different from this trend. How did you obtain the maximum force, just a single SMD trajectory? If so, I wouldn't put a lot of faith in it necessarily. Umbrella sampling is a more robust method than a single pull. You can use large numbers of pulling simulations and apply Jarzynski's equation to calculate free energy, but there are distinct caveats (although I suppose there are caveats with any method). -Justin yes. the max force is obtained from single SMD trajectory. So in this case we dont have to worry about the correction between max. force and free energy. I found one of my free energy result is 2 times larger than the previous result, where they have applied Jarzynski's equation. vijay. -- 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] pulling force vs free energy
Vijayaraj wrote: Message: 4 Date: Wed, 16 Nov 2011 09:34:02 -0500 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] pulling force vs free energy To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4ec3c9da.7040...@vt.edu mailto:4ec3c9da.7040...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Vijayaraj wrote: Hi, What is the relation between pulling force and free energy of binding. can we relate the maximum pulling force with the free energy. for example, 2 systems has the maximum pulling force and free energy as below from umbrella sampling and g_wham analysis, max. forcefree energy system 1 147042 system 2 164732 system 2 has higher pulling force than system 1 and the free energy result is different from this trend. How did you obtain the maximum force, just a single SMD trajectory? If so, I wouldn't put a lot of faith in it necessarily. Umbrella sampling is a more robust method than a single pull. You can use large numbers of pulling simulations and apply Jarzynski's equation to calculate free energy, but there are distinct caveats (although I suppose there are caveats with any method). -Justin yes. the max force is obtained from single SMD trajectory. So in this case we dont have to worry about the correction between max. force and free energy. I found one of my free energy result is 2 times larger than the previous result, where they have applied Jarzynski's equation. SMD is path-dependent, while a true DeltaG is a path-independent quantity. Hence why you cannot easily connect the two. Convergence in sampling and limitations in each technique make it sometimes hard to compare the results that others have obtained with other methods. Proper data collection for Jarzynski's method requires exhaustive sampling, which is often hard to obtain (not a blind criticism of others' work, just a fact). -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/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] calculate potentials of structure
Dear all, I am wondering if there is a way to calculate the potential of a given RNA structure? No minimization, no simulation, but calculate the potential. -- Best, Liang Liu -- 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] pulling force vs free energy
I agree with Justin. I have tried myself several SMD simulations for ligand binding studies. I tried 500 simulations and not sure if they are enough. Further, the path dependence is very important part. For different paths that you can try, look at McCammon group's paper in JACS 128, 3019-3026. There are several other papers too, but this discusses about various methods that you can try to get the pmf using Jarzynski On Wed, Nov 16, 2011 at 9:25 AM, Justin A. Lemkul jalem...@vt.edu wrote: Vijayaraj wrote: Message: 4 Date: Wed, 16 Nov 2011 09:34:02 -0500 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] pulling force vs free energy To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org** Message-ID: 4ec3c9da.7040...@vt.edu mailto:4EC3C9DA.7040400@vt.**edu4ec3c9da.7040...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Vijayaraj wrote: Hi, What is the relation between pulling force and free energy of binding. can we relate the maximum pulling force with the free energy. for example, 2 systems has the maximum pulling force and free energy as below from umbrella sampling and g_wham analysis, max. forcefree energy system 1 147042 system 2 164732 system 2 has higher pulling force than system 1 and the free energy result is different from this trend. How did you obtain the maximum force, just a single SMD trajectory? If so, I wouldn't put a lot of faith in it necessarily. Umbrella sampling is a more robust method than a single pull. You can use large numbers of pulling simulations and apply Jarzynski's equation to calculate free energy, but there are distinct caveats (although I suppose there are caveats with any method). -Justin yes. the max force is obtained from single SMD trajectory. So in this case we dont have to worry about the correction between max. force and free energy. I found one of my free energy result is 2 times larger than the previous result, where they have applied Jarzynski's equation. SMD is path-dependent, while a true DeltaG is a path-independent quantity. Hence why you cannot easily connect the two. Convergence in sampling and limitations in each technique make it sometimes hard to compare the results that others have obtained with other methods. Proper data collection for Jarzynski's method requires exhaustive sampling, which is often hard to obtain (not a blind criticism of others' work, just a fact). -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] calculate potentials of structure
Liu, Liang wrote: Dear all, I am wondering if there is a way to calculate the potential of a given RNA structure? No minimization, no simulation, but calculate the potential. You can do a single-point energy evaluation with the md integrator and nsteps set to 0. -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/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] MDRun -append error
Hi, all I just restart a simulation with 'mpirun -np 8 mdrun -pd yes -s md_0_1.tpr -cpi state.cpt -append' However, the following error appears: Output file appending has been requested, but some output files listed in the checkpoint file state.cpt are not present or are named differently by the current program: output files present: traj.xtc output files not present or named differently: md_0_1.log md_0_1.edr --- Program mdrun, VERSION 4.5.3 Source code file: ../../../gromacs-4.5.3/src/gmxlib/checkpoint.c, line: 2139 Fatal error: File appending requested, but only 1 of the 3 output files are present For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The two files which can not be found were located in the same directory with 'traj.xtc', and why they can not be found by gromacs? Thanks and best regards, Xianqiang -- Xianqiang Sun Email: xianqi...@theochem.kth.se Division of Theoretical Chemistry and Biology School of Biotechnology Royal Institute of Technology S-106 91 Stockholm, Sweden -- 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] *** Extended deadline Dec 6 *** CfP: 2nd Workshop on Model-driven Approaches for Simulation Engineering (Mod4Sim), in Symposium on Theory of Modeling and Simulation, SCS Spring Sim 2012
*** Deadline Extended to December 6, 2011 *** ** Please submit your abstract before November 25, 2011 * # CALL FOR PAPERS 2nd International Workshop on Model-driven Approaches for Simulation Engineering part of the Symposium on Theory of Modeling and Simulation (SCS SpringSim 2012) # March 26-29, 2012, Orlando, FL (USA) http://www.sel.uniroma2.it/Mod4Sim12 # # Papers Due: *** December 6, 2011 ** Extended # Accepted papers will be published in the conference proceedings and archived # in the ACM Digital Library, IEEE Xplorer and IEEE CS Digital Library. # The Symposium is co-sponsored by IEEE. # The workshop aims to bring together experts in model-based, model- driven and software engineering with experts in simulation methods and simulation practitioners, with the objective to advance the state of the art in model-driven simulation engineering. Model-driven engineering approaches provide considerable advantages to software systems engineering activities through the provision of consistent and coherent models at different abstraction levels. As these models are in a machine readable form, model-driven engineering approaches can also support the exploitation of computing capabilities for model reuse, programming code generation, and model checking, for example. The definition of a simulation model, its software implementation and its execution platform form what is known as simulation engineering. As simulation systems are mainly based on software, these systems can similarly benefit from model-driven approaches to support automatic software generation, enhance software quality, and reduce costs, development effort and time-to-market. Similarly to systems and software engineering, simulation engineering can exploit the capabilities of model-driven approaches by increasing the abstraction level in simulation model specifications and by automating the derivation of simulator code. Further advantages can be gained by using modeling languages, such as UML and SysML – but not exclusively those. For example, modeling languages can be used for descriptive modeling (to describe the system to be simulated), for analytical modeling (to specify analytically the simulation of the same system), and for implementation modeling (to define the respective simulator). A partial list of topics of interest includes: * model-driven simulation engineering processes * requirements modeling for simulation * domain specific languages for modeling and simulation * model transformations for simulation model building * model transformations for simulation model implementation * model-driven engineering of distributed simulation systems * relationship between metamodeling standards (e.g., MOF, Ecore) and distributed simulation standards (e.g., HLA, DIS) * metamodels for simulation reuse and interoperability * model-driven technologies for different simulation paradigms (discrete event simulation, multi-agent simulation, sketch-based * simulation, etc.) * model-driven methods and tools for performance engineering of simulation systems * simulation tools for model-driven software performance engineering * model-driven technologies for simulation verification and validation * model-driven technologies for data collection and analysis * model-driven technologies for simulation visualization * Executable UML * Executable Architectures * SysML / Modelica integration * Simulation Model Portability and reuse * model-based systems verification and validation * simulation for model-based systems engineering To stimulate creativity, however, the workshop maintains a wider scope and welcomes contributions offering original perspectives on model- driven engineering of simulation systems. +++ On-Line Submissions and Publication +++ We invite paper submissions in three forms: 1. Full paper (max 8 pages), describing innovative research results. These papers are eligible for the best paper award and may be invited for an extended version in a special issue of the SCS SIMULATION journal. 2. Work-in-progress paper (max 6 pages), describing novel research ideas and promising work that have not yet been fully evaluated. 3. Short paper (max 6 pages), describing industrial and hands-on experience on any relevant area (i.e. military, government, space, etc.). All the papers must be submitted through the SCS conference management systems (http://www.softconf.com/scs/DEVS12/), selecting the Mod4Sim track in the Submission Categories section. All the submitted papers must be in PDF format and must conform to
[gmx-users] Re: Restarting a crashed run
Hi, I was running a simulation of 10ns which crashed in between at 1.7 ns due to power failure. I used the following command to restart the simulation form that point: mdrun -s topol.tpr -cpi state.cpt -append After checking the file md_0_1.log and others , I am getting data only for those 1.7ns . How can I retrieve the data for the other half of the simulation that I restarted ?? -- Bharat -- 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] MDRun -append error
On Wed, Nov 16, 2011 at 4:11 PM, xianqiang xianqiang...@126.com wrote: Hi, all I just restart a simulation with 'mpirun -np 8 mdrun -pd yes -s md_0_1.tpr -cpi state.cpt -append' However, the following error appears: Output file appending has been requested, but some output files listed in the checkpoint file state.cpt are not present or are named differently by the current program: output files present: traj.xtc output files not present or named differently: md_0_1.log md_0_1.edr --- Program mdrun, VERSION 4.5.3 Source code file: ../../../gromacs-4.5.3/src/gmxlib/checkpoint.c, line: 2139 Fatal error: File appending requested, but only 1 of the 3 output files are present For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The two files which can not be found were located in the same directory with 'traj.xtc', and why they can not be found by gromacs? Maybe they are not readable? Can you look at the log file (e.g. using less)? Roland Thanks and best regards, Xianqiang -- Xianqiang Sun Email: xianqi...@theochem.kth.se Division of Theoretical Chemistry and Biology School of Biotechnology Royal Institute of Technology S-106 91 Stockholm, Sweden -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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: Restarting a crashed run
On Wed, Nov 16, 2011 at 7:57 PM, bharat gupta bharat.85.m...@gmail.comwrote: Hi, I was running a simulation of 10ns which crashed in between at 1.7 ns due to power failure. I used the following command to restart the simulation form that point: mdrun -s topol.tpr -cpi state.cpt -append After checking the file md_0_1.log and others , I am getting data only for those 1.7ns . How can I retrieve the data for the other half of the simulation that I restarted ?? Check for Restarting from line in log and errors warnings in the log and the output file. Without more information we can't help. Roland -- Bharat -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] H bonds
Greeting i looking for residues forming Hydrogen bonds with one residue,i can't get that. When using -hbm i get an xpm file that contain existence of hbond over time without any indication about who's the other residues.(it is just binary existence) is there a way to get residues engaged in the bond (with occupancy rate if possible) -- 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] H bonds
larif sofiene wrote: Greeting i looking for residues forming Hydrogen bonds with one residue,i can't get that. Have you tried using an index group that specifies the residue of interest? When using -hbm i get an xpm file that contain existence of hbond over time without any indication about who's the other residues.(it is just binary existence) The index file produced with the -hbn flag maps to the existence matrix in hbmap.xpm. -Justin is there a way to get residues engaged in the bond (with occupancy rate if possible) -- 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/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] H bonds
Greeting i looking for residues forming Hydrogen bonds with one residue,i can't get that. When using -hbm i get an xpm file that contain existence of hbond over time without any indication about who's the other residues.(it is just binary existence) You can check the bonds index created by g_hbond -hbn . -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- 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] Fwd: Restarting a crashed run
Hi, I was running a simulation of 10ns which crashed in between at 1.7 ns due to power failure. I used the following command to restart the simulation form that point: mdrun -s topol.tpr -cpi state.cpt -append After checking the file md_0_1.log and others , I am getting data only for those 1.7ns . How can I retrieve the data for the other half of the simulation that I restarted ?? -- Bharat -- 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: Re: Positive potential energy for TFE solvent
On 16/11/2011 5:02 PM, Harpreet Basra wrote: Hi Mark, Sorry my last mail was incomplete...here is the complete one! On 16/11/2011 1:18 AM, Harpreet Basra wrote: Hi Mark, Thanks for the quick reply. But i have already done what u suggested. On 15/11/2011 6:06 PM, Harpreet Basra wrote: Hi I am still stuck with same problem of obtaining positive potential energy. On 11/11/2011 5:07 PM, Harpreet Basra wrote: Hi I am trying to generate an equilibrated box of 216 TFE molecules.To generate the 216 TFE molecule box i performed following steps: A suggested workflow can be found here http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation I have been following this link only. 1) I got the tfe.gro file and created a cubic box of edge length = 0.516 nm containing 1 TFE molecule (at its center), using the following command: editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516 I chose this length because in the tfe.gro file dimensions of the TFE molecule are 0.516 0.516 0.516. That's not a good reason. Choose a volume and shape that makes sense for your target density. Cubic probably doesn't make sense when a rectangular shape is possible. Then you'll probably want to choose -nbox differently later. I chose a rectangular box too. still i get a positive value for PE and moreover all the molecules move towards two opposite walls of the box. I am not sure that the way I am using the genconf command is the correct way. because I have tried every other possibility for not getting a positive potential, with no success. So here are my .gro file and the topology file for TFE. *tfe.gro file* 7 1TFE F1T 1 0.444 0.344 0.246 1TFE CT 2 0.334 0.245 0.246 1TFE F2T3 0.350 0.160 0.364 1TFE F3T4 0.350 0.160 0.127 1TFE CH2T 5 0.187 0.326 0.246 1TFE OT 6 0.075 0.220 0.246 1TFE HT 7 -0.019 0.266 0.246 0.49174 0.49174 0.49174 topology file [ moleculetype ] ; Name nrexcl TFE 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 FTFE1 TFE F1T 1 -0.170 18.9984 2 CTFE1 TFE CT10.452 12.0110 3 FTFE1 TFE F2T 1 -0.170 18.9984 4 FTFE1 TFE F3T 1 -0.170 18.9984 5 CHTFE 1 TFE CH2T 10.273 14.0270 6 OTFE 1 TFE OT 1 -0.625 15.9994 7 H 1 TFE HT 1 0.410 1.0080 [ bonds ] ; ai aj fu c0, c1, ... 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3 2 5 2 0.153 715.0 0.153 715.0 ; C1 C2 5 6 2 0.143 818.0 0.143 818.0 ; C2 O 6 7 2 0.100 1570.0 0.100 1570.0 ; O H [ pairs ] ; ai aj fu c0, c1, ... 1 6 1 ; F1 O 2 7 1 ; C1 H 3 6 1 ; F2 O 4 6 1 ; F3 O [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H and to construct a box of TFE solvent i took the tfe.gro file and replicated the TFE molecule by using genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6 can u plz suggest is it that I am using genconf in a wrong way that it is causing this problem? I am not sure how many molecules (-nbox option in genconf) should i keep in the box in order to get a mass density of 1383g/L for TFE. That link says Work out how much volume a single molecule would have in the box of your chosen density and size. Useeditconf http://www.gromacs.org/editconfto place a box of that size around your single molecule. It does not seem to me that you have done this. Mark I did place the *single
Re: [gmx-users] import force field
On 16/11/2011 5:00 AM, Liu, Liang wrote: The tabulated potentials I am using is non-bonded interactions. The question is the application of these potentials will only modify the force field, e.g. amber03, or will take place of the force field? The force field is more than the non-bonded interactions. So the use of tables for some non-bonded potentials modifies those parts of the force field. You will have a significant burden of proof that such a modification is valid. Mark On Mon, Nov 14, 2011 at 6:40 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 15/11/2011 9:33 AM, Liu, Liang wrote: I have a serial of tabulated potentials with the name of *.xvg, which are the function of atom distance. I am wondering how to use them in gromacs simulation? Will that replace the force field, e.g. amber03? Thanks. There are sections in the manual that describe the use of tabulated potentials for either bonded or non-bonded interactions. Such tables modify the force field in the expected manner. Mark -- 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 -- Best, Liang Liu -- 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
