Re: [gmx-users] 1-week gromacs test at 112x12 cores
2011/10/6 Matthew Zwier mczw...@gmail.com Hi, If you don't get any takers, you could always just make a huge box of water (which usually dominates explicit-solvent MD costs) and run it. That way, you could scale up the size of the box arbitrarily to achieve good parallelization across that many cores. I'm not sure that'd be scientifically useful, but it sounds like it would fit your business needs just fine. Thank you for your suggestion. Fortunately Gromacs has an active community: I've received multiple replies already, so anybody who's still thinking of replying is too late. Regards, Maik On Thu, Oct 6, 2011 at 9:43 AM, Maik Nijhuis maik.nijh...@clustervision.com wrote: Dear Gromacs users, For one of our customers I have to test a cluster using a parallel application that runs for 1 week on 113 nodes with 12 cores each. The nodes have 20GB memory available. A large Gromacs simulation would be ideal. Unfortunately, I do not have a proper large input file for Gromacs. Since I don't like wasting power and CPU cycles, I'd like to ask you if anyone has a large input file that will keep the cluster busy for one week. I will run the simulation for free using Gromacs 4.5.5, and send you the output. Please send me an email when you're interested. First come, first serve. Regards, Maik Nijhuis -- [image: clustervision_logo.png] Dr. Maik Nijhuis HPC Benchmark Specialist Direct: +31 20 407 7556 Skype: maiknijhuis maik.nijh...@clustervision.com ClusterVision BV Nieuw-Zeelandweg 15B 1045 AL Amsterdam The Netherlands Tel: +31 20 407 7550 Fax: +31 84 759 8389 www.clustervision.com clustervision_logo.gif-- 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] Regarding Density
*Dear All, Please somebody tell me in what way the gromacs calculate the density for given no. of molecules and volume of the box. I generated solvent box using genbox_d command line. Is it right that I can scale the solvent box according to density of my interest after generating box using genbox_d command line?* *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- 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] Ligand scattered out of the protein
Dear Sir, I am doing simulation work with protein-ligand complex (3 ligands). I modeled the protein using modeller, their ligand (two) was translated from the template and one them were docked by autodock 4.2. The protein and ligand coordinates were generated as described by the manual. the ligand particles were scattered out of the pocket when I was doing configuration (editconf -bt triclinic -f trp1.pdb -o trp2.pdb -d 0.85). I was using GROMOS96 43a1 force field. Please help me to get out of this problem. -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- 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: atoms jumps from its native position in protein
Hi i am trying to study protein-ligand interaction. at the end of the simulation, the visualization via- VMD shows, some of the atoms suddenly jumped from its place to another space for a short time and comes back to its position connected by huge lines. i dont have any idea what is the real technical term to describe that. i am not sure where i am making mistake. could any one suggest this how to tackle this problem. thanks Parthiban -- 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: atoms jumps from its native position in protein
Parthiban Marimuthu wrote: Hi i am trying to study protein-ligand interaction. at the end of the simulation, the visualization via- VMD shows, some of the atoms suddenly jumped from its place to another space for a short time and comes back to its position connected by huge lines. i dont have any idea what is the real technical term to describe that. i am not sure where i am making mistake. could any one suggest this how to tackle this problem. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -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] (no subject)
Oh, thanks! On Thu, Oct 6, 2011 at 7:59 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Janani Ganesan wrote: Hi, Thanks for the reply! I tried the rates, and only the terminal with positive rate gets pulled. The first and the last amino acids are spatially oriented one behind the other. I think defining a vector might work better, but I am not sure why nothing happens when I define a pull_vec1 and pull_vec2. Am I missing anything? When setting distance as the pull_geometry, only pull_dim is used; pull_vec is ignored. If you want to define vectors, use the direction pull_geometry. -Justin Thanks, Sai On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Sai Janani Ganesan wrote: Hi, I am trying to pull the first from the last amino acid of a protein to completely unfold the protein in the X direction. I chose the middle amino acid as the reference, and the groups get pulled in the same direction or opposite direction (which is what I want) depending on the trial. I am trying to find a definite method to completely unfold it. I define a different vector (pull_vec1 and pull_vec2) with +x and -x values and that does not even pull the protein I tried using only pull_group1 and pull_group2, without a reference, and neither groups get pulled. I chose different references, I do have some success but I don't think it is the best way to do it. How do I pull the N and C terminal apart, by simultaneously pulling them in opposite directions?Why is my vector definition wrong? This is my pull code: pull= umbrella pull_geometry = distance pull_dim= Y N N pull_start = yes pull_ngroups= 2 pull_group0 = Chain-C pull_group1 = Chain-B pull_group2 = Chain-A %pull_vec1 = -31 0 0 %pull_vec2 = 31 0 0 I suspect the % signs will mess things up, but probably will give a fatal error, if nothing else. pull_rate1 = 0.002pull_k1 = 1000pull_rate2 = 0.002 pull_k2 = 1000 Here's the problem. You're telling the two pulled groups to move in the same direction. With distance geometry, the selections are a bit more simplistic. If you set pull_rate1 to -0.002 and pull_rate2 to 0.002, the groups will be pulled in opposite directions. Otherwise, you're just towing your protein along in the box. -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 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://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-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users 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/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- /Every sentence I utter must be understood not as an affirmation but as a question. - Niels Bohr/ -- ==**== 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/**
[gmx-users] grompp error
Dear all, I generated the molecule topology from antechamber and then coverted to gromcas topology. When I tried to use grompp first it gave me this error : there is no such molecule type SOL, so I checked the topology file and found out there was no #include tip3p.itp . so I added this to the topology file, so the topology file looked like this: ; oht.top created by rdparm2gmx.pl Thu Oct 6 22:24:42 IST 2011 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon c3c3 0. 0. A 3.39967e-01 4.57730e-01 h1h1 0. 0. A 2.47135e-01 6.56888e-02 cfcf 0. 0. A 3.39967e-01 3.59824e-01 haha 0. 0. A 2.59964e-01 6.27600e-02 caca 0. 0. A 3.39967e-01 3.59824e-01 hoho 0. 0. A 0.0e+00 0.0e+00 cece 0. 0. A 3.39967e-01 3.59824e-01 osos 0. 0. A 3.1e-01 7.11280e-01 hchc 0. 0. A 2.64953e-01 6.56888e-02 ohoh 0. 0. A 3.06647e-01 8.80314e-01 n3n3 0. 0. A 3.25000e-01 7.11280e-01 [ moleculetype ] ; Namenrexcl solute 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 c3 1OHTC10 1 -0.08830 12.00 2 c3 1OHT C9 2 -0.04620 12.00 3 ce 1OHT C8 3 -0.04600 12.00 4 ca 1OHTC11 4 -0.05100 12.00 5 ca 1OHTC16 5 -0.11090 12.00 6 ca 1OHTC15 6 -0.12900 12.00 7 ca 1OHTC14 7 -0.12960 12.00 8 ca 1OHTC13 8 -0.13230 12.00 9 ca 1OHTC12 9 -0.12440 12.00 10 cf 1OHT C7 100.00410 12.00 11 ca 1OHT C1 11 -0.08660 12.00 12 ca 1OHT C2 12 -0.07710 12.00 13 ca 1OHT C3 13 -0.15850 12.00 14 ca 1OHT C4 140.12410 12.00 15 oh 1OHT O4 15 -0.49780 16.00 16 ca 1OHT C5 16 -0.21770 12.00 17 ca 1OHT C6 17 -0.08360 12.00 18 ca 1OHTC17 18 -0.09110 12.00 19 ca 1OHTC18 19 -0.08080 12.00 20 ca 1OHTC19 20 -0.16050 12.00 21 ca 1OHTC20 210.13280 12.00 22 os 1OHTO20 22 -0.32490 16.00 23 c3 1OHTC23 230.12760 12.00 24 c3 1OHTC24 240.17240 12.00 25 n3 1OHTN24 25 -0.74670 14.00 26 c3 1OHTC25 260.16000 12.00 27 c3 1OHTC26 270.16650 12.00 28 ca 1OHTC21 28 -0.20950 12.00 29 ca 1OHTC22 29 -0.07840 12.00 30 h1 1OHT H263 300.00150 1.00 31 h1 1OHT H262 310.04950 1.00 32 h1 1OHT H261 320.04480 1.00 33 h1 1OHT H253 330.03530 1.00 34 h1 1OHT H252 340.00500 1.00 35 h1 1OHT H251 350.05060 1.00 36 h1 1OHT H242 360.02390 1.00 37 h1 1OHT H241 370.07020 1.00 38 h1 1OHT H232 380.05310 1.00 39 h1 1OHT H231 390.03440 1.00 40 hc 1OHT H103 400.04260 1.00 41 hc 1OHT H102 410.03010 1.00 42 hc 1OHT H101 420.03390 1.00 43 ho 1OHTHO4 430.41810 1.00 44 hc 1OHTH92 440.04990 1.00 45 hc 1OHTH91 450.05550 1.00 46 ha 1OHT H6 460.13840 1.00 47 ha 1OHT H5 470.13260 1.00 48 ha 1OHT H3 480.15160 1.00 49 ha 1OHTH22 490.13540 1.00 50 ha 1OHTH21 500.13480 1.00 51 ha 1OHT H2 51
Re: [gmx-users] CHARMM 36 force field
Hi Giovanni, Rather than me just provide you with an mdp file I would suggest that you go through the Klauda paper with a copy of the online GROMACS mdp options open (http://manual.gromacs.org/online/mdp_opt.html). This way you should be able to work out what the appropriate setting are yourself using this online help. This should be far more useful for you in the long term. Of course I am happy to answer any specific questions you have about the choices that are still unclear to you after you have tried this (although most should be pretty clear I think). Or, if you have already done this and you are still unsure about an mdp option you will have to be more specific in your question. Cheers Tom Giovanni Mancini wrote: Dear Tom, Thank you very much for your answer. I am aware of the paper you suggested but it is not clear for all mdp parameters. My intent is the simulation of a small organic molecule into the DPPC membrane making use of the CHARMM36 force field. There are significant differences when I change some mdp parameters, according to the advice from the gmx-user list. If there is a checked set of the above parameters that are really work with the NPT ensemble, may I have access to it? Best regards Giovanni -- Dr Thomas Piggot University of Southampton, UK. -- 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] Question about Justin's Free Energy Tutorial
I don't think this is a question about new free energy code -- I think this is asking about the fact if you can do a free energy calculation by specifying the A and B variables in the topology, instead of using the MDP coupl-moltype arguments. This is actually the way free energy calculations were managed before 4.0, and is still supported. The answer is yes, though it requires some experience with what's going on -- and I don't have time to document it all quite right now, as it's described relatively thoroughly in the manual. The one difference is that the coupl-moltype keywords makes it easy to decouple molecules (turn off the intermolecular but not intramolecular energies) from their environment, which is very hard (and sometimes impossible) to do by changing A and B states. If you want to turn off all interactions, then you can do it very straightforwardly by changing the top files. Best, Michael On Thu, Oct 6, 2011 at 2:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: Fabian Casteblanco wrote: Hello Justin, I have a question about your tutorial. If I want to mutate one small group of a molecule, I would have to not provide 'couple_lambda0' and 'couple_lambda1', correct? I would essentially have to follow sec 5.7.4 in the Gromacs manual and I have to actually provide all state A variable and all state B variables. Gromacs would calculate the new B state parameters for bond lengths, angles, etc, correct? Are there any other major differences to account for? I have never attempted FEP with the new free energy code. Try a simple test system first and make sure it works as expected. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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] order parameter
Hi, I want to calculate order parameter for POPC lipid. After reading the comments made by Justin and Chris about g_order, i would like to compare my results from both g_order and vmd tcl script which will compute order parameters from real hydrogen atoms. Below is the link I found for vmd tcl script for order parameter: http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-12867/orderparam2.tcl Please can I know if this is the rite script or is there any other vmd tcl script for calculating order parameter. Kind Regards, chetan. Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] snap shot
Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I run the simulation for 20 ns. I want to save snap-shot at 5ns, 10ns, 15ns and 20ns. I don't want to save snap shot for 128 ion-pairs. How can I take average over 128 ion pairs and save snap shot for a single ion pair. Basically I want to use classical md geometry for quatum chemical calculation. I am using Gromacs 4.0.7 version. Thanks Nilesh -- 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] grompp error
On 8/10/2011 12:35 AM, Chunxia Gao wrote: Dear all, I generated the molecule topology from antechamber and then coverted to gromcas topology. When I tried to use grompp first it gave me this error : there is no such molecule type SOL, so I checked the topology file and found out there was no #include tip3p.itp . so I added this to the topology file, so the topology file looked like this: ; oht.top created by rdparm2gmx.pl Thu Oct 6 22:24:42 IST 2011 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon c3c3 0. 0. A 3.39967e-01 4.57730e-01 h1h1 0. 0. A 2.47135e-01 6.56888e-02 cfcf 0. 0. A 3.39967e-01 3.59824e-01 haha 0. 0. A 2.59964e-01 6.27600e-02 caca 0. 0. A 3.39967e-01 3.59824e-01 hoho 0. 0. A 0.0e+00 0.0e+00 cece 0. 0. A 3.39967e-01 3.59824e-01 osos 0. 0. A 3.1e-01 7.11280e-01 hchc 0. 0. A 2.64953e-01 6.56888e-02 ohoh 0. 0. A 3.06647e-01 8.80314e-01 n3n3 0. 0. A 3.25000e-01 7.11280e-01 [ moleculetype ] ; Namenrexcl solute 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 c3 1OHTC10 1 -0.08830 12.00 2 c3 1OHT C9 2 -0.04620 12.00 3 ce 1OHT C8 3 -0.04600 12.00 4 ca 1OHTC11 4 -0.05100 12.00 5 ca 1OHTC16 5 -0.11090 12.00 6 ca 1OHTC15 6 -0.12900 12.00 7 ca 1OHTC14 7 -0.12960 12.00 8 ca 1OHTC13 8 -0.13230 12.00 9 ca 1OHTC12 9 -0.12440 12.00 10 cf 1OHT C7 100.00410 12.00 11 ca 1OHT C1 11 -0.08660 12.00 12 ca 1OHT C2 12 -0.07710 12.00 13 ca 1OHT C3 13 -0.15850 12.00 14 ca 1OHT C4 140.12410 12.00 15 oh 1OHT O4 15 -0.49780 16.00 16 ca 1OHT C5 16 -0.21770 12.00 17 ca 1OHT C6 17 -0.08360 12.00 18 ca 1OHTC17 18 -0.09110 12.00 19 ca 1OHTC18 19 -0.08080 12.00 20 ca 1OHTC19 20 -0.16050 12.00 21 ca 1OHTC20 210.13280 12.00 22 os 1OHTO20 22 -0.32490 16.00 23 c3 1OHTC23 230.12760 12.00 24 c3 1OHTC24 240.17240 12.00 25 n3 1OHTN24 25 -0.74670 14.00 26 c3 1OHTC25 260.16000 12.00 27 c3 1OHTC26 270.16650 12.00 28 ca 1OHTC21 28 -0.20950 12.00 29 ca 1OHTC22 29 -0.07840 12.00 30 h1 1OHT H263 300.00150 1.00 31 h1 1OHT H262 310.04950 1.00 32 h1 1OHT H261 320.04480 1.00 33 h1 1OHT H253 330.03530 1.00 34 h1 1OHT H252 340.00500 1.00 35 h1 1OHT H251 350.05060 1.00 36 h1 1OHT H242 360.02390 1.00 37 h1 1OHT H241 370.07020 1.00 38 h1 1OHT H232 380.05310 1.00 39 h1 1OHT H231 390.03440 1.00 40 hc 1OHT H103 400.04260 1.00 41 hc 1OHT H102 410.03010 1.00 42 hc 1OHT H101 420.03390 1.00 43 ho 1OHTHO4 430.41810 1.00 44 hc 1OHTH92 440.04990 1.00 45 hc 1OHTH91 450.05550 1.00 46 ha 1OHT H6 460.13840 1.00 47 ha 1OHT H5 470.13260 1.00 48 ha 1OHT H3 480.15160 1.00 49 ha 1OHTH22 490.13540 1.00 50 ha
