Re: [gmx-users] No such moleculetype NA+
Hello Shikha Replace NA+ with NA in your topol.top file. It will solve the problem as it recognise NA for NA+. Thanks Yuvraj IIIT Hyderabad On Sun, Dec 26, 2010 at 12:26 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: Replicating an experiment (David van der Spoel) 2. RE: Replicating an experiment (NG HUI WEN) 3. average pressure too high (sreelakshmi ramesh) 4. No such moleculetype NA+ (shikha agarwal) -- Forwarded message -- From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sat, 25 Dec 2010 22:55:34 +0100 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.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
Re: [gmx-users] Replicating an experiment
On 26/12/2010 4:37 AM, 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 Do be aware that density will change if you do NPT at different T, and you'll need to re-equilibrate regardless. Mark 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.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. -- 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] topolbuild1_3 install problem
Hi all I downloaded topolbuild1_3 from the GROMACS website, and I run the command as follows: path: home/buct/topolbuild1_3 ” # tar -xvf topolbuild1_3.tgz #make -f Makefile ; (intel CPU) there were no any error messages. then I write export PATH=$PATH:/home/buct/topolbuild1_3 into etc/profile(root) ``` But When I type topolbuild -h I get command not found,and I don't know how to deal it. can anyone tell me to install the topolbuild1_3 correctly? Thank you! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] topolbuild1_3 install problem
Hi all I downloaded topolbuild1_3 from the GROMACS website, and I run the command as follows: path: home/buct/topolbuild1_3 ” # tar -xvf topolbuild1_3.tgz #make -f Makefile ; (intel CPU) there were no any error messages. then I write export PATH=$PATH:/home/buct/topolbuild1_3 into etc/profile(root) ``` But When I type topolbuild -h I get command not found,and I don't know how to deal it. can anyone tell me to install the topolbuild1_3 correctly? Thank you! xiaodu -- 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] average pressure too high
Hi, what is the standard deviation and drift? Are you sure this is a significant difference to 1? Roland On Sun, Dec 26, 2010 at 12:28 AM, sreelakshmi ramesh sree.laks...@research.iiit.ac.in wrote: 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 -- 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] amb2gmx.pl file
Hi Xiaodu, The fudgeLJ under defaults should be 1.0 for GLYCAM. I'm unable to check my own files right now so can't compare. When you run grompp check in the output that fudge is set to 1.0. So there will be no protein in your simulation correct? I think there is a way to do mixed scaling in gromacs but I haven't looked into it. Oliver 2010/12/25 gromacs564 gromacs...@126.com 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 typeBchargeB 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
[gmx-users] Re: average pressure too high
On Sun, Dec 26, 2010 at 12:28 AM, sreelakshmi ramesh sree.laks...@research.iiit.ac.in wrote: 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. I believe pressure is something that one should not perceive very seriously if he/she wants to succeed with MD simulations... :-) Dr. Vitaly V. Chaban | skype: vvchaban Department of Chemistry | email: v.cha...@rochester.edu University of Rochester | email: vvcha...@gmail.com Rochester, NY 14627-0216 | email: cha...@univer.kharkov.ua United States of America | chem.rochester.edu/~prezhdo_group -- 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] number of DD cells
Hi, I am following umbrella sampling tutorial for my membrane protein system. While running continuous pulling simulation (mdrun). under step five: Generating Configurations of the tutorial. I get the below error. The system ran initially but corrupted very soon with warning The X-size of the box (4.800448) times the triclinic skew factor (1.00) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.20) I am using 64 cores with -npme = 16. I haven't set any -dds. My system box size is 6 x 6 x 12 nm Please can I know what might be the problem. 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), Dr. Ulrich Krafft (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
Re: [gmx-users] How to suppress the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group
Hi, Mark, Thanks for the reply. As suggested, I tried a water in vacuum case. Initially the water droplet is a cubic 4nm-by-4nm-by-4nm water box, located in the middle of the simulation box. Everywhere else is just vacuum. The simulation box size is 8nm by 8nm by 8nm. SPC/E model is used to describe interaction between water molecules. Such system is first equilibrated with steep option. The mdrun simulation goes with no problem with parallel running on 32 cpus, even though there are occasionaly one or two water molecules move very fast (Mean square displacement being 200 times fast than bulk water) in the vacuum. When I switch to 64 cpus, the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group appears. Below is the parameter file I'm using. integrator = md tinit= 0 dt = 0.002 nsteps = 500 comm-mode= Linear nstcomm = 1 comm-grps= energygrps = nstlist = 1 ns_type = grid pbc = xyz rlist= 1.5 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.5 epsilon-r= 1 vdw-type = Cut-off ;Switch rvdw-switch = 1.0 rvdw = 1.5 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no Tcoupl = nose-hoover tc-grps = System tau_t= 1.0 ref_t= 300 Pcoupl = no ;Parrinello-Rahman ;no ;berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = no gen_temp = 300 gen_seed = 2008 constraints = none constraint-algorithm = Lincs Shake-SOR= no shake-tol= 1e-04 lincs-order = 4 lincs-warnangle = 30 energygrp_excl = Is there any parameters configuration wrong with the simulation? Or is there any way to go around this error? Any tip is appreciated. Thank you. Best, Yanbin -- Message: 1 Date: Thu, 02 Dec 2010 17:24:18 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] How to suppress the error X particles communicatedto PME node Y are more than a cell length out of the domain decomposition cell of their charge group To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4cf73b92.40...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/12/2010 4:16 PM, WU Yanbin wrote: Dear GMXers, I'm running a simulation of water contact angle measurement on top of graphite surface. Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simulation to develop a spherical shape. An error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group was encountered. And I have read the suggested solutions at the link below http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group . I guess the reason for this error in my case is because of the vacuum such that the water molecules at the boundary of the droplet can move fast. I have check the trajectory and the simulation is OK. I doubt the simulation is OK. This error message is one of several that can happen when the system is not well-enough conditioned for the MD to be stable. See www.gromacs.org/Documentation/Terminology/Blowing_Up. Here, you have atoms moving much faster than GROMACS was engineered to expect. You should be confident that a water drop in a vacuum, and your graphite surface are both stable on their own before you try the wetting simulation. For this situation, is there a way of suppressing this error? Or what else can I do? Work out why it's poorly conditioned. 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?
[gmx-users] number of DD cells
Hi, To my earlier post on number of DD cells.i included -dds 0.6 and everything seems to run fine. Is this the possible solution to the error or is there other way to handle this warning ? 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), Dr. Ulrich Krafft (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] umbrella sampling
Hi, I am working on membrane protein. In umbrella sampling tutorial...we saw the pulling of the peptide A away from peptide B. I want to pull the peptide deep into the hydrophobic core of the bilayer from outside (solvent environment). Please can someone suggest me how to go about this. 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), Dr. Ulrich Krafft (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
Re: [gmx-users] How to suppress the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group
On 27/12/2010 9:22 AM, WU Yanbin wrote: Hi, Mark, Thanks for the reply. As suggested, I tried a water in vacuum case. Initially the water droplet is a cubic 4nm-by-4nm-by-4nm water box, located in the middle of the simulation box. Everywhere else is just vacuum. The simulation box size is 8nm by 8nm by 8nm. SPC/E model is used to describe interaction between water molecules. Such system is first equilibrated with steep option. The mdrun simulation goes with no problem with parallel running on 32 cpus, even though there are occasionaly one or two water molecules move very fast (Mean square displacement being 200 times fast than bulk water) in the vacuum. OK, that sounds like behaviour that might be expected... some molecules evaporate. Check the trajectory to be confident this is the situation. When I switch to 64 cpus, the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group appears. The most plausible reason for this is that the above evaporated molecules are moving so fast that they're doing what the error message says - travelling more than width of a box in one integration step. The DD implementation is predicated on that being impossible. You might succeed by arranging for the largest possible internal DD cell diameter, i.e. a 4x4x4 DD. mdrun -npme 0 might choose this, otherwise use the hidden options to mdrun (use mdrun -hidden) to use that DD with -npme 0. Otherwise, you'll need to accept the fact that there are engineering constraints on efficient parallelization algorithms, and not every situation can be catered for. For example, a simulation of a bulk LJ fluid would fail if you used so many processors that the cell diameter was too small with respect to the distribution of particle speeds. Mark Below is the parameter file I'm using. integrator = md tinit= 0 dt = 0.002 nsteps = 500 comm-mode= Linear nstcomm = 1 comm-grps= energygrps = nstlist = 1 ns_type = grid pbc = xyz rlist= 1.5 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.5 epsilon-r= 1 vdw-type = Cut-off ;Switch rvdw-switch = 1.0 rvdw = 1.5 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no Tcoupl = nose-hoover tc-grps = System tau_t= 1.0 ref_t= 300 Pcoupl = no ;Parrinello-Rahman ;no ;berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = no gen_temp = 300 gen_seed = 2008 constraints = none constraint-algorithm = Lincs Shake-SOR= no shake-tol= 1e-04 lincs-order = 4 lincs-warnangle = 30 energygrp_excl = Is there any parameters configuration wrong with the simulation? Or is there any way to go around this error? Any tip is appreciated. Thank you. Best, Yanbin -- Message: 1 Date: Thu, 02 Dec 2010 17:24:18 +1100 From: Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au Subject: Re: [gmx-users] How to suppress the error X particles communicatedto PME node Y are more than a cell length out of the domain decomposition cell of their charge group To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4cf73b92.40...@anu.edu.au mailto:4cf73b92.40...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/12/2010 4:16 PM, WU Yanbin wrote: Dear GMXers, I'm running a simulation of water contact angle measurement on top of graphite surface. Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simulation to develop a spherical shape. An error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group was encountered. And I have read the suggested solutions at the link below
Re: [gmx-users] number of DD cells
On 27/12/2010 7:51 AM, Poojari, Chetan wrote: Hi, I am following umbrella sampling tutorial for my membrane protein system. While running continuous pulling simulation (mdrun). under step five: Generating Configurations of the tutorial. I get the below error. The system ran initially but corrupted very soon with warning The X-size of the box (4.800448) times the triclinic skew factor (1.00) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.20) I am using 64 cores with -npme = 16. I haven't set any -dds. My system box size is 6 x 6 x 12 nm That's a large box deformation... 6nm to 4.8nm. I'd say your system is probably blowing up, and that -dds 0.6 is hiding the symptoms. Try running on fewer processors to see whether when the DD box size is larger whether you get other explosion symptoms. 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] topolbuild1_3 install problem
On 26/12/2010 10:07 PM, gromacs564 wrote: Hi all I downloaded topolbuild1_3 from the GROMACS website, and I run the command as follows: path: home/buct/topolbuild1_3 ?? # tar -xvf topolbuild1_3.tgz #make -f Makefile ; (intel CPU) there were no any error messages. then I write export PATH=$PATH:/home/buct/topolbuild1_3 into etc/profile(root) Don't mess with root files unless it's essential. You have your own .profile file for a reason. ``` But When I type topolbuild -h I get command not found,and I don't know how to deal it. The path of the *current* shell has to be right. Editing the files that set the path for *new* shells doesn't do anything to the current shell. can anyone tell me to install the topolbuild1_3 correctly? Does it provide documentation, and have you read it? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] number of DD cells
Hi Mark, I ran on 48 processors.the error is: The X-size of the box (5.312040) times the triclinic skew factor (1.00) is smaller than the number of DD cells (6) times the smallest allowed cell size (0.885281) Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham [mark.abra...@anu.edu.au] Sent: 27 December 2010 00:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] number of DD cells On 27/12/2010 7:51 AM, Poojari, Chetan wrote: Hi, I am following umbrella sampling tutorial for my membrane protein system. While running continuous pulling simulation (mdrun). under step five: Generating Configurations of the tutorial. I get the below error. The system ran initially but corrupted very soon with warning The X-size of the box (4.800448) times the triclinic skew factor (1.00) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.20) I am using 64 cores with -npme = 16. I haven't set any -dds. My system box size is 6 x 6 x 12 nm That's a large box deformation... 6nm to 4.8nm. I'd say your system is probably blowing up, and that -dds 0.6 is hiding the symptoms. Try running on fewer processors to see whether when the DD box size is larger whether you get other explosion symptoms. 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 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), Dr. Ulrich Krafft (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
Re: [gmx-users] number of DD cells
Poojari, Chetan wrote: Hi Mark, I ran on 48 processors.the error is: The X-size of the box (5.312040) times the triclinic skew factor (1.00) is smaller than the number of DD cells (6) times the smallest allowed cell size (0.885281) I would say this further confirms Mark's suspicions. Whatever you're doing to the system is causing it to rapidly collapse, a behavior that is now independent of the number of DD cells. -Justin Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham [mark.abra...@anu.edu.au] Sent: 27 December 2010 00:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] number of DD cells On 27/12/2010 7:51 AM, Poojari, Chetan wrote: Hi, I am following umbrella sampling tutorial for my membrane protein system. While running continuous pulling simulation (mdrun). under step five: Generating Configurations of the tutorial. I get the below error. The system ran initially but corrupted very soon with warning The X-size of the box (4.800448) times the triclinic skew factor (1.00) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.20) I am using 64 cores with -npme = 16. I haven't set any -dds. My system box size is 6 x 6 x 12 nm That's a large box deformation... 6nm to 4.8nm. I'd say your system is probably blowing up, and that -dds 0.6 is hiding the symptoms. Try running on fewer processors to see whether when the DD box size is larger whether you get other explosion symptoms. 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 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), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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
Poojari, Chetan wrote: Hi, I am working on membrane protein. In umbrella sampling tutorial...we saw the pulling of the peptide A away from peptide B. I want to pull the peptide deep into the hydrophobic core of the bilayer from outside (solvent environment). Please can someone suggest me how to go about this. The same principles as in the tutorial apply. Choose a reference group (membrane), a pull group (peptide), and a pull direction. You'll have to empirically adjust pull rate, force constant, etc to properly treat your system. -Justin 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), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] Replicating an experiment
Thanks Mark, message noted:) -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Sunday, December 26, 2010 6:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Replicating an experiment On 26/12/2010 4:37 AM, 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 Do be aware that density will change if you do NPT at different T, and you'll need to re-equilibrate regardless. Mark 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.se http://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. -- 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
