[gmx-users] Re:gmx-users Digest, Vol 80, Issue 164
Hi Alan , Oliver I have obtained the gromacs format files by amb2gmx.pl script, but I am not sure if this flies are correct , because all of the [pairs](1-4 interaction) are zero in gromacs top files. I don't know whether this files are correct or not. Would you give me some advice? Thank your very much. all the best xiaodu - ; lambda.top created by rdparm2gmx.pl Fri Dec 24 10:22:31 CST 2010 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon HOHO 0. 0. A 0.0e+00 0.0e+00 H1H1 0. 0. A 2.47135e-01 6.56888e-02 OSOS 0. 0. A 3.1e-01 7.11280e-01 CGCG 0. 0. A 3.39967e-01 4.57730e-01 H2H2 0. 0. A 2.29317e-01 6.56888e-02 OHOH 0. 0. A 3.06647e-01 8.80314e-01 [ moleculetype ] ; Namenrexcl solute 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 HO 1ROHHO1 10.44500 1.00 2 OH 1ROH O1 2 -0.63900 16.00 3 CG 24GA C1 30.50900 12.00 4 H2 24GA H1 40.0 1.00 5 CG 24GA C2 50.24600 12.00 6 H1 24GA H2 60.0 1.00 7 OH 24GA O2 7 -0.71300 16.00 8 HO 24GAH2O 80.43700 1.00 9 CG 24GA C3 90.28600 12.00 10 H1 24GA H3 100.0 1.00 11 OH 24GA O3 11 -0.69900 16.00 12 HO 24GAH3O 120.42700 1.00 13 CG 24GA C4 130.25400 12.00 14 H1 24GA H4 140.0 1.00 15 CG 24GA C5 150.28300 12.00 16 H1 24GA H5 160.0 1.00 17 OS 24GA O5 17 -0.57400 16.00 18 CG 24GA C6 180.27600 12.00 19 H1 24GAH61 190.0 1.00 20 H1 24GAH62 200.0 1.00 21 OH 24GA O6 21 -0.68200 16.00 22 HO 24GAH6O 220.41800 1.00 23 OS 24GA O4 23 -0.46800 16.00 24 CG 30GA C1 240.50900 12.00 25 H2 30GA H1 250.0 1.00 26 CG 30GA C2 260.24600 12.00 27 H1 30GA H2 270.0 1.00 28 OH 30GA O2 28 -0.71300 16.00 29 HO 30GAH2O 290.43700 1.00 30 CG 30GA C3 300.28600 12.00 31 H1 30GA H3 310.0 1.00 32 OH 30GA O3 32 -0.69900 16.00 33 HO 30GAH3O 330.42700 1.00 34 CG 30GA C4 340.25400 12.00 35 H1 30GA H4 350.0 1.00 36 OH 30GA O4 36 -0.71000 16.00 37 HO 30GAH4O 370.43600 1.00 38 CG 30GA C5 380.28300 12.00 39 H1 30GA H5 390.0 1.00 40 OS 30GA O5 40 -0.57400 16.00 41 CG 30GA C6 410.27600 12.00 42 H1 30GAH61 420.0 1.00 43 H1 30GAH62 430.0 1.00 44 OH 30GA O6 44 -0.68200 16.00 45 HO 30GAH6O 450.41800 1.00 [ bonds ] ; aiaj funct r k 1 2 1 9.6000e-02 4.6275e+05 2122 1 9.6000e-02 4.6275e+05 1819 1 1.0900e-01 2.8451e+05 1820 1 1.0900e-01 2.8451e+05 1516 1 1.0900e-01 2.8451e+05 [ pairs ] ; aiaj funct 2 6 1 1 4 1 1 5 1 1 17 1 5 23 1 3 11 1 3 13 1 3 18 1 40 44 1 36 40 1 36
Re: [gmx-users] Nose-hoover T-coupling in REMD
On 25/12/10 02:12, Qin Qiao wrote: Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? As far as I know v-rescale should generate a correct ensemble. -- Massimo Sandal, Ph.D. http://devicerandom.org -- 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] How can I ...?
Dear All I want to generate .top and .gro files for protein-ligand complex. there are many problems,can every body guide me? Actually it is my M.sc thesis and it has taken much time of me. problems: 1-after using PRODRG server the vector boxes for are not the same 2-ligand's coordinates change very much,then my structure is not the original one that I wanted(I think it is because of box vector) 3-there are a few atom types which is not familiar for grompp Actually I don't know what I can do with this condition If any of you can generate them for me please say me to send complex.pdb file in his/her email. Thanks in advance for your guidance -- 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: Help regarding Membrane simulation
Unfortunately I am neither a free help service, nor know anything about membrane simulations. Please consider reading some textbook and/or tutorial material (search the web) and please ask focussed questions on an appropriate mailing list. Mark Original Message Subject:Help regarding Membrane simulation Date: Sat, 25 Dec 2010 00:22:38 -0800 From: Gugan kothandan gugan...@gmail.com To: mark.abra...@anu.edu.au Dear Abraham, Am Gugan and doing my graduation in Bioinformatics. Currently am practising membrane simulation technique in GROMACS. I am facing some problem while running it. I read your query in the GMX-users. I got your mail id from it. Am a beginer in this one. Please send me some protocol for simulating proteins in lipid layer. Am facing some error in topology section. Hopes for the best from you. Thanking you in anticipation. Yours sincerely, Gugan.K -- 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] generate .top file
On 25/12/2010 2:32 PM, shikha agarwal wrote: hello Merry Christmas. this is my topol_pope.top file ; Include chain topologies #include forcefield.itp #include pope.itp ; Include water topology #include spc.itp ; Include ion topologies #include ions.itp ; System specifications [ system ] 340-Lipid POPE Bilayer [ molecules ] ; molecule name nr. POPE 340 SOL 6729 but it should contain protein molecule .what should be topology file ,, how to generate that for system.gro according to tutorial. my protein has 344 molecules . I tried to use g_x2top but it is not available for gromos53a6. You need an .itp file for your protein, and to #include it, and to adjust the [molecules] field suitably. 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] Nose-hoover T-coupling in REMD
I'm not sure, since actually kinetic energy should have fluctuation, and the v-rescaling may suppress the fluctuation.. 2010/12/25 ms deviceran...@gmail.com On 25/12/10 02:12, Qin Qiao wrote: Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? As far as I know v-rescale should generate a correct ensemble. -- Massimo Sandal, Ph.D. http://devicerandom.org -- 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] dssp problem
On 25/12/2010 11:03 PM, mustafa bilsel wrote: Hi Justin, maybe I am making a mistake with installation. What I am doing is this: I am creating a diretory called DSSP, then I write rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ http://rsync.cmbi.ru.nl/dssp/ /home/m/DSSP/ on the terminal, and then file transfer starts. Then I write export DSSP=/home/m/DSSP/dssp (pointing the exe file). In above procedures there is NO INSTALLATION. If any installation is required? We don't support DSSP. Please read their instructions and follow them. If you can't follow them, please communicate the problem to them so they can fix it. Another important thing is that I couldn't copy dssp to anywhere with copy dssp /. command, but I can do it cp -r dssp / It means that dssp isnot a file, it seems a folder. And I also see uncompressed zip explanation near the dssp. OK, so if it's a folder, open it and look for the executable to work out its fully-qualified name... I have written axactly what I did so far. No, you've used some frustrating ellipses, instead of copying and pasting from your terminal, thereby leaving us the option of presuming you've done something wrong. Mark Maybe it will help you to understand the mistake. Thank you for your kind interests best wishes Mustafa -- 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 can I ...?
On 25/12/2010 11:21 PM, mohsen ramezanpour wrote: Dear All I want to generate .top and .gro files for protein-ligand complex. there are many problems,can every body guide me? Actually it is my M.sc thesis and it has taken much time of me. Yep, research is difficult and time-consuming and hard to do without a live person of whom to ask questions in real time. problems: 1-after using PRODRG server the vector boxes for are not the same 2-ligand's coordinates change very much,then my structure is not the original one that I wanted(I think it is because of box vector) 3-there are a few atom types which is not familiar for grompp Actually I don't know what I can do with this condition If any of you can generate them for me please say me to send complex.pdb file in his/her email. Sounds like you are embarked on a http://www.gromacs.org/Documentation/How-tos/Parameterization problem that should only be attempted by experienced users who can put in the time to do it properly. At the very least, you should do all the tutorial material you can find, and do some other MD study before needing to worry about developing novel parameters. 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] Nose-hoover T-coupling in REMD
On 25/12/2010 1:12 PM, Qin Qiao wrote: Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? I'm quite curious how to choose the frequency of the T-coupling in REMD. Though it seems the higher the frequency, the more accurate T will be, I wonder whether it will get artifacts for in MD run.. since the warning in Gromacs says tau_t should be 20 times bigger than dt*nsttcouple.. Consider what you mean by accurate T. You actually wish to sample from a given constant temperature ensemble. However that ensemble does not show its average T at every instant - the conserved quantity is not actually temperature. What you want is the right average T and the right fluctuations. Probably you want to read the literature for the T-coupling algorithms to learn more about the details here... Probably I should also too :-) Mark Best, Qin 2010/12/25 David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se On 12/24/10 6:40 PM, ms wrote: On 24/12/10 12:26, David van der Spoel wrote: I'm not an expert, but isn't Berendsen usually not used because it doesn't give a correct ensemble? I may be partial because I personally know Giovanni Bussi, but it seems from what I've heard that v-rescale is the best choice usually. V-rescale is a good choice. Berendsen not only gives you the wrong ensemble but it also biases the energy distribution to lower energies. Out of curiosity: why is it still supported in GROMACS? Wouldn't lead to less confusion if it is removed? :) It's still useful for equilibration, e.g. gas to liquid conversion. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se sp...@gromacs.org mailto:sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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
[gmx-users] g-dist
Dear All How can we measure the distance between COM of two molecules?of course in vector form! thanks in advance -- 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] Replicating an experiment
Dear all, Merry Xmas! I have a very quick question here which i'd like to pick your brain on, would really appreciate a reply. I am planning to replicate an experiment that I have carried out. Just wondering what is the best way to do it? I am thinking of changing the starting velocity of my system by setting a random number e.g 23412445 etc in the gen_seed section as below, not sure if it is meaningful to do so? gen_vel = yes gen_temp = 300.0 gen_seed = random number Thank you for your input! HW This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- 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] Optimization of the box size during an energy minimization?
Yeah! Energy minimization with pressure coupling. Is this possible? Ting On 12/24/2010 5:04 AM, Terry wrote: On Fri, Dec 24, 2010 at 5:36 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 24/12/2010 5:17 AM, MyLinkka wrote: Does anybody know if it is possible to optimize the box size during an energy minimization in Gromacs? Optimize for what criterion? Can I make pressure coupling if it's possible? Do you mean energy minimization with pressure coupling? Terry Sure, that's in the manual and covered in tutorials. Mark Is there a workaround if there is no direct way? Thanks! Ting -- 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] Replicating an experiment
On 2010-12-25 15.05, NG HUI WEN wrote: Dear all, Merry Xmas! I have a very quick question here which i'd like to pick your brain on, would really appreciate a reply. I am planning to replicate an experiment that I have carried out. Just wondering what is the best way to do it? I am thinking of changing the starting velocity of my system by setting a random number e.g 23412445 etc in the gen_seed section as below, not sure if it is meaningful to do so? gen_vel = yes gen_temp = 300.0 gen_seed = random number Thank you for your input! That will work fine, if you simulate long enough. Consider that the starting structure may also influence how different your results will be, e.g. for a protein in water. For liquids there is no such problem. You can do a simulation and slightly elevated temperature and pick structures from that with a different random seed, in order to randomize your simulations even more. HW This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Optimization of the box size during an energy minimization?
Hi Mark, Forgive me asking a question that may be obvious for experienced GMX users. I want to quickly verify a problem against some other software, so I temporarily turn to Gromacs. It would be nice if you could point me out where to find the relevant tutorial or manual chapter. I couldn't find the solution after a quick browsing the manual. I'm sorry that I do not intend to spend too much time on learning Gromacs. Thank you for understanding! Ting On 12/23/2010 10:36 PM, Mark Abraham wrote: On 24/12/2010 5:17 AM, MyLinkka wrote: Does anybody know if it is possible to optimize the box size during an energy minimization in Gromacs? Optimize for what criterion? Can I make pressure coupling if it's possible? Sure, that's in the manual and covered in tutorials. Mark Is there a workaround if there is no direct way? Thanks! Ting -- 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] generate .top file
Mark Abraham wrote: On 25/12/2010 2:32 PM, shikha agarwal wrote: hello Merry Christmas. this is my topol_pope.top file ; Include chain topologies #include forcefield.itp #include pope.itp ; Include water topology #include spc.itp ; Include ion topologies #include ions.itp ; System specifications [ system ] 340-Lipid POPE Bilayer [ molecules ] ; molecule name nr. POPE 340 SOL 6729 but it should contain protein molecule .what should be topology file ,, how to generate that for system.gro according to tutorial. my protein has 344 molecules . I tried to use g_x2top but it is not available for gromos53a6. You need an .itp file for your protein, and to #include it, and to adjust the [molecules] field suitably. Or use the approach described in the membrane protein tutorial, wherein pdb2gmx is used to produce the protein .top, which is then modified to #include the relevant chain topologies. It appears that the OP is claiming to use the tutorial but is not actually following its instructions. -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] Optimization of the box size during an energy minimization?
MyLinkka wrote: Yeah! Energy minimization with pressure coupling. Is this possible? No. There are no velocities in EM, and hence no kinetic energy, no virial, and thus no pressure coupling. -Justin Ting On 12/24/2010 5:04 AM, Terry wrote: On Fri, Dec 24, 2010 at 5:36 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 24/12/2010 5:17 AM, MyLinkka wrote: Does anybody know if it is possible to optimize the box size during an energy minimization in Gromacs? Optimize for what criterion? Can I make pressure coupling if it's possible? Do you mean energy minimization with pressure coupling? Terry Sure, that's in the manual and covered in tutorials. Mark Is there a workaround if there is no direct way? Thanks! Ting -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- 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] Nose-hoover T-coupling in REMD
On 25/12/10 02:12, Qin Qiao wrote: Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? As far as I know v-rescale should generate a correct ensemble. On 25/12/10 12:40, Qin Qiao wrote: I'm not sure, since actually kinetic energy should have fluctuation, and the v-rescaling may suppress the fluctuation.. (PLEASE don't top post!!) Well, the thermostat author, who I happen to know, says it generates the right ensemble. :) I'm not an expert so I can't say if it's true, but if you like you can read the original papers, linked here: http://sites.google.com/site/giovannibussi/Research/algorithms#TOC-A-stochastic-velocity-rescaling-the cheers, m. -- Massimo Sandal, Ph.D. http://devicerandom.org -- 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] Replicating an experiment
Thank you David for your prompt and useful reply :) I am in fact simulating a membrane protein. It's good to know I can use the generate-new-starting-velocity method. But, do you mind to elaborate a bit more what you mean by if you simulate long enough? I would like to try your suggestion of picking a random structure from an elevated temperature simulation. Can I achieve that by taking my existing membrane protein system, 1) pass it through grompp with a new mdp (with higher temperature) to produce a new .tpr file 2) simulate the system for a period (perhaps 1 ns) 3) take any frame / final structure 4) pass it through grompp again (with original mdp with temperature 300K, gen_seed = -1) to produce the .tpr file for my replicate? Thanks very much indeed!! From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel Sent: Sat 12/25/2010 10:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Replicating an experiment On 2010-12-25 15.05, NG HUI WEN wrote: Dear all, Merry Xmas! I have a very quick question here which i'd like to pick your brain on, would really appreciate a reply. I am planning to replicate an experiment that I have carried out. Just wondering what is the best way to do it? I am thinking of changing the starting velocity of my system by setting a random number e.g 23412445 etc in the gen_seed section as below, not sure if it is meaningful to do so? gen_vel = yes gen_temp = 300.0 gen_seed = random number Thank you for your input! That will work fine, if you simulate long enough. Consider that the starting structure may also influence how different your results will be, e.g. for a protein in water. For liquids there is no such problem. You can do a simulation and slightly elevated temperature and pick structures from that with a different random seed, in order to randomize your simulations even more. HW This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se http://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. winmail.dat-- 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] amb2gmx.pl file
Hi Alan , Oliver I have obtained the gromacs format files by amb2gmx.pl script, but I am not sure if this flies are correct , because all of the [pairs](1-4 interaction) are zero in gromacs top files. I don't know whether this files are correct or not. Would you give me some advice? Thank your very much. all the best xiaodu - ; lambda.top created by rdparm2gmx.pl Fri Dec 24 10:22:31 CST 2010 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon HOHO 0. 0. A 0.0e+00 0.0e+00 H1H1 0. 0. A 2.47135e-01 6.56888e-02 OSOS 0. 0. A 3.1e-01 7.11280e-01 CGCG 0. 0. A 3.39967e-01 4.57730e-01 H2H2 0. 0. A 2.29317e-01 6.56888e-02 OHOH 0. 0. A 3.06647e-01 8.80314e-01 [ moleculetype ] ; Namenrexcl solute 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 HO 1ROHHO1 10.44500 1.00 2 OH 1ROH O1 2 -0.63900 16.00 3 CG 24GA C1 30.50900 12.00 4 H2 24GA H1 40.0 1.00 5 CG 24GA C2 50.24600 12.00 6 H1 24GA H2 60.0 1.00 7 OH 24GA O2 7 -0.71300 16.00 8 HO 24GAH2O 80.43700 1.00 9 CG 24GA C3 90.28600 12.00 10 H1 24GA H3 100.0 1.00 11 OH 24GA O3 11 -0.69900 16.00 12 HO 24GAH3O 120.42700 1.00 13 CG 24GA C4 130.25400 12.00 14 H1 24GA H4 140.0 1.00 15 CG 24GA C5 150.28300 12.00 16 H1 24GA H5 160.0 1.00 17 OS 24GA O5 17 -0.57400 16.00 18 CG 24GA C6 180.27600 12.00 19 H1 24GAH61 190.0 1.00 20 H1 24GAH62 200.0 1.00 21 OH 24GA O6 21 -0.68200 16.00 22 HO 24GAH6O 220.41800 1.00 23 OS 24GA O4 23 -0.46800 16.00 24 CG 30GA C1 240.50900 12.00 25 H2 30GA H1 250.0 1.00 26 CG 30GA C2 260.24600 12.00 27 H1 30GA H2 270.0 1.00 28 OH 30GA O2 28 -0.71300 16.00 29 HO 30GAH2O 290.43700 1.00 30 CG 30GA C3 300.28600 12.00 31 H1 30GA H3 310.0 1.00 32 OH 30GA O3 32 -0.69900 16.00 33 HO 30GAH3O 330.42700 1.00 34 CG 30GA C4 340.25400 12.00 35 H1 30GA H4 350.0 1.00 36 OH 30GA O4 36 -0.71000 16.00 37 HO 30GAH4O 370.43600 1.00 38 CG 30GA C5 380.28300 12.00 39 H1 30GA H5 390.0 1.00 40 OS 30GA O5 40 -0.57400 16.00 41 CG 30GA C6 410.27600 12.00 42 H1 30GAH61 420.0 1.00 43 H1 30GAH62 430.0 1.00 44 OH 30GA O6 44 -0.68200 16.00 45 HO 30GAH6O 450.41800 1.00 [ bonds ] ; aiaj funct r k 1 2 1 9.6000e-02 4.6275e+05 2122 1 9.6000e-02 4.6275e+05 1819 1 1.0900e-01 2.8451e+05 1820 1 1.0900e-01 2.8451e+05 1516 1 1.0900e-01 2.8451e+05 [ pairs ] ; aiaj funct 2 6 1 1 4 1 1 5 1 1 17 1 5 23 1 3 11 1 3 13 1 3 18 1 40 44 1 36 40 1 36
Re: [gmx-users] Replicating an experiment
On 12/25/10 6:37 PM, NG HUI WEN wrote: Thank you David for your prompt and useful reply :) I am in fact simulating a membrane protein. It's good to know I can use the generate-new-starting-velocity method. But, do you mind to elaborate a bit more what you mean by if you simulate long enough? I would like to try your suggestion of picking a random structure from an elevated temperature simulation. Can I achieve that by taking my existing membrane protein system, 1) pass it through grompp with a new mdp (with higher temperature) to produce a new .tpr file 2) simulate the system for a period (perhaps 1 ns) 3) take any frame / final structure 4) pass it through grompp again (with original mdp with temperature 300K, gen_seed = -1) to produce the .tpr file for my replicate? Yes that is what I meant. Of course you should check that your protein is not unfolding, or you membrane going into the wrong phase. Thanks very much indeed!! From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel Sent: Sat 12/25/2010 10:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Replicating an experiment On 2010-12-25 15.05, NG HUI WEN wrote: Dear all, Merry Xmas! I have a very quick question here which i'd like to pick your brain on, would really appreciate a reply. I am planning to replicate an experiment that I have carried out. Just wondering what is the best way to do it? I am thinking of changing the starting velocity of my system by setting a random number e.g 23412445 etc in the gen_seed section as below, not sure if it is meaningful to do so? gen_vel = yes gen_temp = 300.0 gen_seed = random number Thank you for your input! That will work fine, if you simulate long enough. Consider that the starting structure may also influence how different your results will be, e.g. for a protein in water. For liquids there is no such problem. You can do a simulation and slightly elevated temperature and pick structures from that with a different random seed, in order to randomize your simulations even more. HW This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to
RE: [gmx-users] Replicating an experiment
Got it, thanks very much David! :) -Original Message- From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel Sent: Sun 12/26/2010 5:55 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Replicating an experiment On 12/25/10 6:37 PM, NG HUI WEN wrote: Thank you David for your prompt and useful reply :) I am in fact simulating a membrane protein. It's good to know I can use the generate-new-starting-velocity method. But, do you mind to elaborate a bit more what you mean by if you simulate long enough? I would like to try your suggestion of picking a random structure from an elevated temperature simulation. Can I achieve that by taking my existing membrane protein system, 1) pass it through grompp with a new mdp (with higher temperature) to produce a new .tpr file 2) simulate the system for a period (perhaps 1 ns) 3) take any frame / final structure 4) pass it through grompp again (with original mdp with temperature 300K, gen_seed = -1) to produce the .tpr file for my replicate? Yes that is what I meant. Of course you should check that your protein is not unfolding, or you membrane going into the wrong phase. Thanks very much indeed!! From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel Sent: Sat 12/25/2010 10:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Replicating an experiment On 2010-12-25 15.05, NG HUI WEN wrote: Dear all, Merry Xmas! I have a very quick question here which i'd like to pick your brain on, would really appreciate a reply. I am planning to replicate an experiment that I have carried out. Just wondering what is the best way to do it? I am thinking of changing the starting velocity of my system by setting a random number e.g 23412445 etc in the gen_seed section as below, not sure if it is meaningful to do so? gen_vel = yes gen_temp = 300.0 gen_seed = random number Thank you for your input! That will work fine, if you simulate long enough. Consider that the starting structure may also influence how different your results will be, e.g. for a protein in water. For liquids there is no such problem. You can do a simulation and slightly elevated temperature and pick structures from that with a different random seed, in order to randomize your simulations even more. HW This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se
[gmx-users] average pressure too high
Dear users, I did nvt equil and after that npt equilbriation and i am using parinello rahman as the barostat but the prob is even after 200 ps of equil the avg pressure is 1.5 bar .can anybody hepl me out with the issue.Any suggestions please. sree. -- 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] No such moleculetype NA+
hello , this is my ions.itp file for gromos53a6 forcefield [ moleculetype ] ; molnamenrexcl CU11 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1CU1+1CU1CU 11 63.54600 [ moleculetype ] ; molnamenrexcl CU1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1CU2+1CUCU 12 63.54600 [ moleculetype ] ; molnamenrexcl ZN1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1ZN2+1ZNZN 12 65.37000 this is my ions.itp [ moleculetype ] ; molnamenrexcl MG1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1MG2+1MGMG 12 24.30500 [ moleculetype ] ; molnamenrexcl CA1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1CA2+1CACA 12 40.08000 [ moleculetype ] ; molnamenrexcl NA1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1NA+1NANA 11 22.9898 [ moleculetype ] ; molnamenrexcl CL1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1CL-1CLCL 1-1 35.45300 for adding ions I used this command ... genion -s ions.tpr -o system_solv_ions.gro -p grompp.top -pname NA+ -np 11 -nname CL- now when I m doing EM then getting this error grompp -f minim.mdp -c system_solv_ions.gro -p grompp.top -o em.tpr Fatal error: No such moleculetype NA+ help me ! regards: shikha -- 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 such moleculetype NA+
Have a look at the rtp file of the force field u r using for correct representation of the ion used.. With regards, J. John Wesly, FInal Year, B.Tech., Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India. ~WesFaith~ He who desire to learn, pursues towards edification... One who has will to do, finds a way how to do. Have a LEARNING SPREE Desire to learn... Passion to know things... Unravel the mysteries about your abilities... On Sun, Dec 26, 2010 at 12:26 PM, shikha agarwal shikhaiiit...@gmail.comwrote: hello , this is my ions.itp file for gromos53a6 forcefield [ moleculetype ] ; molnamenrexcl CU11 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1CU1+1CU1CU 11 63.54600 [ moleculetype ] ; molnamenrexcl CU1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1CU2+1CUCU 12 63.54600 [ moleculetype ] ; molnamenrexcl ZN1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1ZN2+1ZNZN 12 65.37000 this is my ions.itp [ moleculetype ] ; molnamenrexcl MG1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1MG2+1MGMG 12 24.30500 [ moleculetype ] ; molnamenrexcl CA1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1CA2+1CACA 12 40.08000 [ moleculetype ] ; molnamenrexcl NA1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1NA+1NANA 11 22.9898 [ moleculetype ] ; molnamenrexcl CL1 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1CL-1CLCL 1-1 35.45300 for adding ions I used this command ... genion -s ions.tpr -o system_solv_ions.gro -p grompp.top -pname NA+ -np 11 -nname CL- now when I m doing EM then getting this error grompp -f minim.mdp -c system_solv_ions.gro -p grompp.top -o em.tpr Fatal error: No such moleculetype NA+ help me ! regards: shikha -- 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] dssp problem
http://biskit.pasteur.fr/install/applications/dssp wget ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip unzip dsspcmbi.zip cd dssp ./DsspCompileGCC cd .. sudo mv dssp /usr/local/src/ cd /usr/local/bin sudo ln -s ../src/dssp/dsspcmbi . lina On Sat, Dec 25, 2010 at 8:45 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 25/12/2010 11:03 PM, mustafa bilsel wrote: Hi Justin, maybe I am making a mistake with installation. What I am doing is this: I am creating a diretory called DSSP, then I write rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /home/m/DSSP/ on the terminal, and then file transfer starts. Then I write export DSSP=/home/m/DSSP/dssp (pointing the exe file). In above procedures there is NO INSTALLATION. If any installation is required? We don't support DSSP. Please read their instructions and follow them. If you can't follow them, please communicate the problem to them so they can fix it. Another important thing is that I couldn't copy dssp to anywhere with copy dssp /. command, but I can do it cp -r dssp / It means that dssp isnot a file, it seems a folder. And I also see uncompressed zip explanation near the dssp. OK, so if it's a folder, open it and look for the executable to work out its fully-qualified name... I have written axactly what I did so far. No, you've used some frustrating ellipses, instead of copying and pasting from your terminal, thereby leaving us the option of presuming you've done something wrong. Mark Maybe it will help you to understand the mistake. Thank you for your kind interests best wishes Mustafa -- 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
