[gmx-users] Output of g_hbond
Hi all, I am trying to caluculate number of hydrogen bond in my system using the following command: g_hbond -f model_frame2000.pdb -s md.tpr -n index_water.ndx -num hbnum.xvg Where the file model_frame2000.pdb is the coordinate from a frame during my MD simulation, and the index file （index_water.ndx） contains the index six adjacent tip5p water molecules, see following: 2559 2560 2561 2562 2563 3029 3030 3031 3032 3033 3504 3505 3506 3507 3508 5354 5355 5356 5357 5358 5394 5395 5396 5397 5398 6049 6050 6051 6052 6053 The arrangement of water oxygen is like this (rectangle), which “ - ” indicates the distance is less than 0.35 nm. OW - OW - OW ||| OW - OW - OW The output hbnum.xvg gives @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm -1 4 10 As I know, the 2nd column is the number of Hydrogen bonds, and the 3ird column indicates “the Pairs within 0.35 nm, but with angle 30”. After viewing the stucture in VMD, I found that the number of Hydrogen bond seems to be correct. However, only 7 pairs of water oxygen within 0.35 nm can be found (see above for the schematic drawing of water arrangement), thus “the Pairs within 0.35 nm, but with angle 30”should be 7-4 = 3, which is significantly lower than the value (10) obtained in hbnum.xvg. I don't what's wrong. Thanks Hu Qiu -- 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] Output of g_hbond
On 11/23/11 4:12 PM, Hu Qiu wrote: Hi all, I am trying to caluculate number of hydrogen bond in my system using the following command: g_hbond -f model_frame2000.pdb -s md.tpr -n index_water.ndx -num hbnum.xvg Where the file model_frame2000.pdb is the coordinate from a frame during my MD simulation, and the index file (index_water.ndx)contains the index six adjacent tip5p water molecules, see following: 2559 2560 2561 2562 2563 3029 3030 3031 3032 3033 3504 3505 3506 3507 3508 5354 5355 5356 5357 5358 5394 5395 5396 5397 5398 6049 6050 6051 6052 6053 The arrangement of water oxygen is like this (rectangle), which - indicates the distance is less than 0.35 nm. OW - OW - OW ||| OW - OW - OW The output hbnum.xvg gives @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm -1 4 10 As I know, the 2nd column is the number of Hydrogen bonds, and the 3ird column indicates the Pairs within 0.35 nm, but with angle 30. After viewing the stucture in VMD, I found that the number of Hydrogen bond seems to be correct. However, only 7 pairs of water oxygen within 0.35 nm can be found (see above for the schematic drawing of water arrangement), thus the Pairs within 0.35 nm, but with angle 30should be 7-4 = 3, which is significantly lower than the value (10) obtained in hbnum.xvg. Third column should be simply pairs within 0.35nm, at any angle. I don't what's wrong. Thanks Hu Qiu -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding Simulation of KALP-15 in DPPC
*Dear All, I was following the tutorial for simulating KALP-15 in DPPC. I got stuck in step three. Following the instruction, I created the dppc128.gro file using editconf. To remove the initial periodcity I was trying to use trjconv but I could not do it. Please help me in this regard. * *Thank you* *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
Re: [gmx-users] do_dssp segmentation fault
Hi, On Nov 23, 2011, at 8:24 AM, Alex Jemulin wrote: Thanks for your reply Could you tell me the name of the file to download and how to install it? Please follow the instructions at http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage and http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial. In short: git clone git://git.gromacs.org/gromacs.git git checkout --track -b release-4-5-patches origin/release-4-5-patches If you are using CMake, you can then just install this like the normal .tar.gz distributions from the gromacs home page. If you are using autotools, do a ./bootstrap before the configure step. Best, Carsten Bests Da: Carsten Kutzner ckut...@gwdg.de A: Alex Jemulin alexbioi...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Inviato: Martedì 22 Novembre 2011 13:25 Oggetto: Re: [gmx-users] do_dssp segmentation fault Dear Alex, On Nov 22, 2011, at 9:28 AM, Alex Jemulin wrote: Dear all I'm experiencing the following error in Gromacs 4.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10 give me the following error segmentation fault How can I fix it? I removed a segmentation fault in do_dssp a couple of weeks ago but this is post version 4.5.5. So you need to check out the current release-4-5-patches from the git server. I believe this will fix your problem. Carsten Thank in ad -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] T-coupling
Dear Gromacs Users, I need to simulate two protein structures by Gromacs 5.4.0. For protein A, the net charge is zero so I don't add any ions. All the commands work properly unitil mdrun of the A_pr.tpr: mdrun -s A_pr.tpr -o A_pr.trr -c A_b4md.gro -g pr.log -e pr.edr == the error: too many LINCS warnings For protein B I have to add 4 NA+: grompp -f pr.mdp -c B_b4pr.gro -p B.top -o B_pr.tpr == error: 4 atoms are not part of the T-coupling groups. I checked my pr.mdp file. Tcoup is berendsen. How can I solve these problems? Best regards, Sarah -- 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] T-coupling
On 11/23/11 5:43 PM, sarah k wrote: Dear Gromacs Users, I need to simulate two protein structures by Gromacs 5.4.0. For protein A, the net charge is zero so I don't add any ions. All the commands work properly unitil mdrun of the A_pr.tpr: mdrun -s A_pr.tpr -o A_pr.trr -c A_b4md.gro -g pr.log -e pr.edr == the error: too many LINCS warnings Could be a sign something is going wrong with your system. Did you do a proper energy minimization? Check the gromacs error pages for some more precise indication. http://www.gromacs.org/Documentation/Errors For protein B I have to add 4 NA+: grompp -f pr.mdp -c B_b4pr.gro -p B.top -o B_pr.tpr == error: 4 atoms are not part of the T-coupling groups. Control the groups of your thermostat in your .mdp file. There should be one including the whole system. Check section 7.3.14 of the gromacs manual I checked my pr.mdp file. Tcoup is berendsen. How can I solve these problems? Best regards, Sarah -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Visualizing g_helixorient output
Dear all, I have a follow up question from this recent post http://www.mail-archive.com/gmx-users@gromacs.org/msg45736.html regarding the visualization of g_helixorient output. According to the post, one needs to use xmgrace with -nxy to view the data properly. I have not got the xmgrace program installed and am just wondering if one could use programs like gnuplot (with some special commands perhaps) instead? Thanks! Best wishes, Huiwen 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] Generating topology file
Hi GROMACS users, I have used acpype.py to convert parameter and topology file from amber to gromacs but some of the parameters (angle and dihedral)regarding a particular residue having mercury in it was not generating,please help. Thanks in advance. Madhumita Das -- 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] Generating topology file
I am sorry, but because antechamber will only work with these atoms: C, N, O, S, P, H, F, Cl, Br and I, so acype won't work for Hg. A hack would be to replace Hg by another allowed element. But this is only to give you a hint of what topology and parameters might look like. Then you have to work hard in literature to find parameters and likely make use of RED for getting a more quantum mechanics approach for your parameters and charges. Good luck, Alan On 23 November 2011 10:35, madhumita das madhumita.bioi...@gmail.comwrote: Hi GROMACS users, I have used acpype.py to convert parameter and topology file from amber to gromacs but some of the parameters (angle and dihedral)regarding a particular residue having mercury in it was not generating,please help. Thanks in advance. Madhumita Das -- 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 -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- 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: PDB structure quality
An update: Now for NRG-CING, please see: http://nmr.cmbi.ru.nl/NRG-CING Best, Alan On 3 April 2009 11:31, Alan alanwil...@gmail.com wrote: We've recently announced iCing, which includes whatif as well. Please, take a look at http://nmr.cmbi.ru.nl/cing/Home.html. If it happens that your complex is from NMR and deposit in PDB so you can find it here (http://nmr.cmbi.ru.nl/NRG-CING/index/index.html) already evaluated. Cheers, Alan On Fri, Apr 3, 2009 at 11:00, gmx-users-requ...@gromacs.org wrote: Chih-Ying Lin wrote: HI The program WHATIF can perform a proper validation of the structure. But, it is not free software. Can anyone tell me how to test the protein structure manually or by Gromacs? What is the criteria to determine the quality of the structure? That depends on your objective - but you have to define that. Ultimately some protein structure generated by a piece of software has to match in a relevant way the structure found in biological systems. What that means varies with what experimental information you have available. Various computational tools might assist in estimating that match. Mark -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- 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] gromacs 4.5.3 and GCC 4.1.x
Hi, I want to install standard gromacs 4.5.5 on a new linux machine, prior to installing GPU accelerated gromacs. Looking at the installation instructions I see you recommend not to use GCC 4.1.x series of compilers. A year ago I have installed gromacs 4.5.3 and I don't recall seeing the recommendation of not using the GCC 4.1.x compilers. The gcc version of the computer on which I installed is: /usr/bin/gcc -v == /u/gcc version 4.1.2 20080704 (Red Hat 4.1.2-51). Is there also a problem with gromacs 4.5.3 and GCC 4.1.x? Was I supposed to have trouble installing or running? Is it possible I was able to compile and run but I can't rely on the results I got? Thanks, Efrat -- 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] unity in ffbonded.itp
Dear gromacs developers, I would like to know what is the unity for armonic constraint in ffbonded.itp. In the user manual (Table 5.4) it is written that is kJ mol-1 nm-2 but in the .itp file I read C C 1 0.1525 259408.0 ; new99 I understand that 0.1525 is the equlibrium distance 5in nm) but 259408.0 KJ it is almost high. Maybe the right value is 259408.0 J ? Francesco -- 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] NPT or NVT for calculating averaged experimental parameters
Hi there, Is there any consensus on whether to use NVT or NPT runs for calculating averaged NMR parameters in water at room temperature? I have seen some papers which use NPT, others use NVT. Thanks you, Igor -- 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] CHARMMff using GROMACS 4.5.3
Hi all, I am trying to run a simulation of a protein and ligand system using Gromacs 4.5.3 and CHARMMff. prior to running this system I ran the protein as is with out adding the ligand, and the simulation was fine. Ligand parametrization was done using the SwissParam server. when trying to run EM I got the following error message: Syntax error - File ligand.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Obviously the outputted itp format given by SwissParam is wrong. can anyone direct me as to the changes needed to correct this mistake? Thanks! -- Gideon Lapidoth, M.Sc candidate Hemi Gutman Biophysics Lab Department of Biochemistry Molecular Biology George S. Wise Faculty of Life Sciences Tel Aviv University Israel 69978 http://ashtoret.tau.ac.il/ Tel: (972-3) 640-9824 -- 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: pdb2gmx disulfide bond formation - missing bond, angle, dihedral types with all GROMOS FFs (Tsjerk Wassenaar)
Hi Tsjerk, Thank you for your advice! grompp does not complain (with all three of the previously mentioned versions of GROMACS), but the processed topology, processed.top, also does not have the terms filled in, as I show below for the bonds section: [ bonds ] ; aiaj functc0c1c2c3 ...skipping... 5657 20.1830 5.6200e+06 57 585 2 5859 20.1230 1.6600e+07 ... (This is also true for the angles and dihedrals.) But, I ran some minimization and 100 ps of equilibration (with no position restraints) and viewed the output using Gromacs's ngmx trajectory viewer so that bonds would be drawn based upon the topology and not the proximity of atoms (what e.g., Rasmol does). There does appear to be three disulfide bonds present. I then used g_dist to calculate the distance between the two sulfur atoms in each of the disulfides during that short equilibration. They all came out on average to be 0.2040 nm, which is exactly what the equilibrium bond length would be if it were using the correct bond type. So, while it seems strange to me that they do not appear in the topology (preprocessed or processed), I am reassured that GROMACS really is using the disulfide information with the GROMOS FFs. I appreciate your help. Cheers, Elizabeth Hi Elizabeth, These missing terms are filled in automatically by grompp from the bondtypes, angletypes and dihedraltypes definitions in the *bon.itp. Unless grompp complains about missing terms, you'll be fine. You can check whether everything is okay by writing out a processed topology (grompp -pp) and looking up the bonds.angles/dihedrals there. Cheers, Tsjerk -- 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] problem with extr of g_anaeig
Hi!! I am looking my eigenvectors through the extr command of g_anaeig and I found different pdb files for my 1st vector in the following 3 conditions: gromacs-4.5.5/bin/g_anaeig -f file.xtc -s average.pdb -v eigenvec.trr -n index.ndx -extr -nframes 20 -first 1 -last 1 gromacs-4.5.5/bin/g_anaeig -f file.xtc -s average.pdb -v eigenvec.trr -n index.ndx -extr -nframes 20 -first 1 -last 2 gromacs-4.5.5/bin/g_anaeig -f file.xtc -s average.pdb -v eigenvec.trr -n index.ndx -extr -nframes 20 -first 1 -last 50 Is it normal? They should be the same, don't they? I read an old post related with that but I though it would be solved... Many thanks Agnes -- 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] density
Thanks Prof. Warren From: Dallas Warren dallas.war...@monash.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, November 22, 2011 12:23 AM Subject: RE: [gmx-users] density I don’t do COM calculations, so don’t know directly, but have a read of “g_rdf –h”, method is outlined there and I suspect there are a number of discussions on it within the emailing list archive that you should search. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From:mohammad agha [mailto:mra...@yahoo.com] Sent: Tuesday, 22 November 2011 4:28 AM To: Dallas Warren Subject: Re: [gmx-users] density Dear Prof. Warren Excuse me, may I know that how to obtain the average radial density functions relative to the center of mass with g_rdf? I think these plots are produced by counting the number of selected atoms that are within the x angstrom wide shells around the micelle COM, and I think that I should use from : N= 4 π ρ∫ 0 00 r2 g(r) dr. , but I don't know how to find N and what is the computation carefully? Please help me. Best Regards Sara From:Dallas Warren dallas.war...@monash.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, November 21, 2011 2:04 AM Subject: RE: [gmx-users] density Last bit here, that is probably done using a RDF, which is a probability function, which you can then convert into a number of atoms in each shell. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Sunday, 20 November 2011 5:52 PM To: gmx-users@gromacs.org Subject: [gmx-users] density Dear Prof. I have problems about density. I equilibrated my system consist 500 surfactants and 6 water molecules in martini coarse-grained for 120 ns and my results of g_energy next pr.mdp for density are: average = 907.701 err.est = 0.61 rmsd = 2.54989 tot-drift = -3.4173 I don't know about good quantity of err.est, rmsd and tot-drift for density adjustment? and when my system has been equilibrated? May I know about my problem, please? On the other hand, density distribution for different groups of the system in terms of their distance from micell's COM distance is considered In the articles about surfactants. I think that it is possible with g_density but this program compute the density as the function of box(nm). May I know about this problem, Please? Best Regards sara -- 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] Re: NPT or NVT for calculating averaged experimental parameters
Hi there, Is there any consensus on whether to use NVT or NPT runs for calculating averaged NMR parameters in water at room temperature? I have seen some papers which use NPT, others use NVT. Thanks you, Igor There should be no difference as far as the density is reproduced adequately in both ensembles. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Regarding Simulation of KALP-15 in DPPC
What exactly did you try? What was the result? Actually copy and paste the commands and output. Saying it didn't work is insufficient detail for anyone to help you. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Ravi Kumar Venkatraman Sent: Wednesday, 23 November 2011 7:58 PM To: gmx-users@gromacs.org Subject: [gmx-users] Regarding Simulation of KALP-15 in DPPC Dear All, I was following the tutorial for simulating KALP-15 in DPPC. I got stuck in step three. Following the instruction, I created the dppc128.gro file using editconf. To remove the initial periodcity I was trying to use trjconv but I could not do it. Please help me in this regard. Thank you 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] how to edit a .xvg file?
Hi everyone, I wonder if there is any tool similar to trjconv that can be used to edit a .xvg file? I just want to extract selected data points (like taking data every 10 ps when the original .xvg contains data every 1 ps) and to concatenate .xvg files according to the time of data. Thanks, Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs 4.5.3 and GCC 4.1.x
Efrat Exlrod wrote: Hi, I want to install standard gromacs 4.5.5 on a new linux machine, prior to installing GPU accelerated gromacs. Looking at the installation instructions I see you recommend not to use GCC 4.1.x series of compilers. A year ago I have installed gromacs 4.5.3 and I don't recall seeing the recommendation of not using the GCC 4.1.x compilers. The gcc version of The warning about the gcc compilers has been on the website for several years. the computer on which I installed is: /usr/bin/gcc -v == /u/gcc version 4.1.2 20080704 (Red Hat 4.1.2-51). Is there also a problem with gromacs 4.5.3 and GCC 4.1.x? Was I supposed to have trouble installing or running? As I recall, the bug was in gcc and it led to various random failures of different tools. Perhaps others with more knowledge of the compilers themselves can comment. Upgrading gcc is a good idea; the 4.1.x is quite outdated. Is it possible I was able to compile and run but I can't rely on the results I got? Possible. More likely you would get random instability rather than some hidden inaccuracy. -Justin Thanks, Efrat -- 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] unity in ffbonded.itp
francesco oteri wrote: Dear gromacs developers, I would like to know what is the unity for armonic constraint in ffbonded.itp. In the user manual (Table 5.4) it is written that is kJ mol−1 nm−2 but in the .itp file I read C C 1 0.1525 259408.0 ; new99 The value of 1 indicates a function type (simple harmonic expression). I understand that 0.1525 is the equlibrium distance 5in nm) but 259408.0 KJ it is almost high. Maybe the right value is 259408.0 J ? The quoted units are correct. Verify yourself with the primary literature for the chosen force field (which may require some conversions, i.e. kcal - kJ, Angstrom - nm). -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] CHARMMff using GROMACS 4.5.3
Gideon Lapidoth wrote: Hi all, I am trying to run a simulation of a protein and ligand system using Gromacs 4.5.3 and CHARMMff. prior to running this system I ran the protein as is with out adding the ligand, and the simulation was fine. Ligand parametrization was done using the SwissParam server. when trying to run EM I got the following error message: Syntax error - File ligand.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Obviously the outputted itp format given by SwissParam is wrong. can anyone direct me as to the changes needed to correct this mistake? The .itp file is probably correct but your manner of adding it to your .top is wrong. The topology hierarchy must be observed, so if a new molecule needs new [atomtypes], then they must be #included prior to the declaration of *any* [moleculetype]. Likely your #include statement is simply misplaced, and should be something like: #include charmm27.ff/forcefield.itp #include ligand.itp (remaining protein-related stuff) -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] how to edit a .xvg file?
Yun Shi wrote: Hi everyone, I wonder if there is any tool similar to trjconv that can be used to edit a .xvg file? I just want to extract selected data points (like taking data every 10 ps when the original .xvg contains data every 1 ps) and to concatenate .xvg files according to the time of data. Several options: 1. Use trjconv to reduce output frequency. 2. Use simple scripting or *nix operations to manipulate the resulting .xvg files. Skipping lines in output is trivial for a language like Perl, and concatenation can be done with simple *nix utilities like 'cat' and others. -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] how to edit a .xvg file?
On 24/11/2011 10:31 AM, Yun Shi wrote: Hi everyone, I wonder if there is any tool similar to trjconv that can be used to edit a .xvg file? I just want to extract selected data points (like taking data every 10 ps when the original .xvg contains data every 1 ps) and to concatenate .xvg files according to the time of data. It's usually easiest to re-create the file using the -dt option of the tool. Note that the command that created the .xvg file is recorded in a comment in the file. 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
[gmx-users] Hbond occupancy reference rate
Greeting After doing a gormacs MD simulation and finding Hydrogen bonds,applying Justin script give me the Hbonds occupancy rate,then i have to choose the most representative structure in the simulation and show some of my interesting hydrogen bonds for publication purpose. Should i consider a reference Hbond existence percentage from which bond between two atoms are significantly existent like for example for a hbond occupancy rate of 10% we can say that this hbond has a good chance to exist in reality an effectively participate in the protein phenomena (movement,structure...) and for another hbond occupancy with 0.7% we can safely ignore it because it will not participate in protein behavior. Is there such reference value? thanks for responding. -- 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] Visualizing g_helixorient output
On 23/11/2011 8:59 PM, NG HUI WEN wrote: Dear all, I have a follow up question from this recent post http://www.mail-archive.com/gmx-users@gromacs.org/msg45736.html regarding the visualization of g_helixorient output. According to the post, one needs to use xmgrace with --nxy to view the data properly. I have not got the xmgrace program installed and am just wondering if one could use programs like gnuplot (with some special commands perhaps) instead? Yes, you will be able to generate a plot. See http://www.gromacs.org/Documentation/How-tos/Graphing_Data 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] Visualizing g_helixorient output
Dear Mark, Many thanks for taking the time to answer my question. I've had a look at the link. However, as the g_helixorient output files are a little unconventional-looking, I am not sure if gnuplot could handle them. This is how my bending.xvg file looks like when I view it on my linux terminal 00015.5414686203 13.96718311315.497541904451.833977103234.68 052530289 0.6835690736774.433454036718.259634971625.08707904816 13.33345127117.342966079712.19187068 9392.44664645195 0.2027087807663.6609973907510.3064308167 4.37143564224 0.97176563739812.6073293686 81.100708007866.195884704628.065074920712.996044 16.375751495400 100.07629002.19846844673 3.11483025551 0.6649964451791.770893931395.45 8261489875.118296146392.507099628452.909595012664.06375169754 9.8080854415912.7944087982 2.6745197 7734.585949420931.637694239622.60466551781 0.494560062885 5.879833221442.3917922973617.8020935059 89.386047363378.208717346222.62022781377.18984699249 2.1821160316500 200.152590011.4898967743 14.803553581211.05572509774.956498622895.58 4476947788.459140777595.94662857056 0.607162833214 2.6271879673 8.95005798342.298228740697.87417221 069 0.8924096822747.417117118842.011978149417.29352807999 3.83971619606 0.76795816421515.4690599442 87.566352844273.416061401424.13317489628.33314704895 2.4264836311300 3000012.7444248199 11.35336303716.021839141852.641380071641.24 458372593 0.3753441870212.736594915394.949892997745.81749725342 16.21747779858.222133636474.51266765 5944.294775962837.2541747093212.55032825475.51523017883 4.44073772439.5040454864517.9626598358... ... ... I have played with other options too e.g. axis.dat, center.dat, radius.xvg, rise.xvg, rot.xvg etc. they all look like the above. Any help is very much appreciated. Thanks again, Huiwen From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Thursday, November 24, 2011 10:39 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Visualizing g_helixorient output On 23/11/2011 8:59 PM, NG HUI WEN wrote: Dear all, I have a follow up question from this recent post http://www.mail-archive.com/gmx-users@gromacs.org/msg45736.html regarding the visualization of g_helixorient output. According to the post, one needs to use xmgrace with -nxy to view the data properly. I have not got the xmgrace program installed and am just wondering if one could use programs like gnuplot (with some special commands perhaps) instead? Yes, you will be able to generate a plot. See http://www.gromacs.org/Documentation/How-tos/Graphing_Data Mark 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] how to edit a .xvg file?
Thanks for the reply. In my case, they are the pullf and pullx files from a COM pulling simulation. So does this mean writing a script would be the best way? Thanks, Yun == == -- Message: 5 Date: Wed, 23 Nov 2011 19:04:33 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] how to edit a .xvg file? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ecd8a11.9030...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Yun Shi wrote: Hi everyone, I wonder if there is any tool similar to trjconv that can be used to edit a .xvg file? I just want to extract selected data points (like taking data every 10 ps when the original .xvg contains data every 1 ps) and to concatenate .xvg files according to the time of data. Several options: 1. Use trjconv to reduce output frequency. 2. Use simple scripting or *nix operations to manipulate the resulting .xvg files. Skipping lines in output is trivial for a language like Perl, and concatenation can be done with simple *nix utilities like 'cat' and others. -Justin -- -- Message: 6 Date: Thu, 24 Nov 2011 13:23:02 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] how to edit a .xvg file? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4ecdaa86.7050...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 24/11/2011 10:31 AM, Yun Shi wrote: Hi everyone, I wonder if there is any tool similar to trjconv that can be used to edit a .xvg file? I just want to extract selected data points (like taking data every 10 ps when the original .xvg contains data every 1 ps) and to concatenate .xvg files according to the time of data. It's usually easiest to re-create the file using the -dt option of the tool. Note that the command that created the .xvg file is recorded in a comment in the file. 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
[gmx-users] Re: how to edit a .xvg file?
Sorry for this question. The bash script turned out to be a one-liner. Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Visualizing g_helixorient output
On 24/11/2011 1:50 PM, NG HUI WEN wrote: Dear Mark, Many thanks for taking the time to answer my question. I've had a look at the link. However, as the g_helixorient output files are a little unconventional-looking, I am not sure if gnuplot could handle them. This is how my bending.xvg file looks like when I view it on my linux terminal 00015.5414686203 13.96718311315.497541904451.833977103234.68 052530289 0.6835690736774.433454036718.25963497162 5.0870790481613.33345127117.342966079712.19187068 9392.44664645195 0.2027087807663.66099739075 10.30643081674.37143564224 0.97176563739812.6073293686 81.100708007866.195884704628.065074920712.996044 16.375751495400 100.07629002.19846844673 3.11483025551 0.6649964451791.770893931395.45 8261489875.118296146392.507099628452.90959501266 4.063751697549.8080854415912.7944087982 2.6745197 7734.585949420931.637694239622.60466551781 0.4945600628855.879833221442.3917922973617.8020935059 89.386047363378.208717346222.62022781377.18984699249 2.1821160316500 200.152590011.4898967743 14.803553581211.05572509774.956498622895.58 4476947788.459140777595.94662857056 0.607162833214 2.6271879673 8.95005798342.298228740697.87417221 069 0.8924096822747.417117118842.01197814941 7.293528079993.83971619606 0.76795816421515.4690599442 87.566352844273.416061401424.13317489628.33314704895 2.4264836311300 3000012.7444248199 11.35336303716.021839141852.641380071641.24 458372593 0.3753441870212.736594915394.94989299774 5.8174972534216.21747779858.222133636474.51266765 5944.294775962837.2541747093212.5503282547 5.51523017883 4.44073772439.5040454864517.9626598358... ... ... This is not really a GROMACS question... but with gnuplot: plot 'file.xvg' using 1:2, 'file.xvg' using 1:3, ... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: how to edit a .xvg file?
Hi Yun, I would not have expected otherwise :p Would you mind sharing your solution? Cheers, Tsjerk On Nov 24, 2011 4:54 AM, Yun Shi yunsh...@gmail.com wrote: Sorry for this question. The bash script turned out to be a one-liner. Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] grompp line too long error
I was trying to setup a simulation for membrane in DPPC lipid bilayer following this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I successfully generated the .gro file for the system.But when I tried grompp to generate the .tpr file,I got the error message shown below: --- Program grompp, VERSION 4.5.4 Source code file: string2.c, line: 105 Fatal error: An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I use strace to trace the sys call of grompp,I have found that grompp opened gurgle.dat,and ended up reading gurgle.dat as text file,while gurgle.dat is a binary file,then grompp throwed the fatal error message. What could be the cause of this problem? -- 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 line too long error
On 24/11/2011 3:45 PM, 杨伟 wrote: I was trying to setup a simulation for membrane in DPPC lipid bilayer following this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I successfully generated the .gro file for the system.But when I tried grompp to generate the .tpr file,I got the error message shown below: --- Program grompp, VERSION 4.5.4 Source code file: string2.c, line: 105 Fatal error: An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I use strace to trace the sys call of grompp,I have found that grompp opened gurgle.dat,and ended up reading gurgle.dat as text file,while gurgle.dat is a binary file,then grompp throwed the fatal error message. What could be the cause of this problem? I would be more suspicious of your input files than anything else. Make sure you edit them with a sensible text editor that uses useful line endings. Can you use grompp successfully on a simple test case with files you haven't edited? 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] grompp line too long error
Hi [insert name here], Try putting an empty gurgle.dat in your working directory to see if that is the problem. If it's not, can you provide additional information regarding your system and gromacs installation? Cheers, Tsjerk On Nov 24, 2011 5:50 AM, 杨伟 20104227...@suda.edu.cn wrote: I was trying to setup a simulation for membrane in DPPC lipid bilayer following this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I successfully generated the .gro file for the system.But when I tried grompp to generate the .tpr file,I got the error message shown below: --- Program grompp, VERSION 4.5.4 Source code file: string2.c, line: 105 Fatal error: An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I use strace to trace the sys call of grompp,I have found that grompp opened gurgle.dat,and ended up reading gurgle.dat as text file,while gurgle.dat is a binary file,then grompp throwed the fatal error message. What could be the cause of this problem? -- 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] how to edit a .xvg file?
Dear gmx users, Is centroid to centroid clustering method available in Gromacs? I want to use this method to cluster my molecules? ROB -- 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: do remd in npt enmable with warning :pressure scaling more than 1%, mu: 1.01087 1.01087 1.01087
dear teacher, when i do remd in npt enmable , there are mang warning like this “Step 520013 Warning: pressure scaling more than 1%, mu: 1.01311 1.01311 1.01311 Step 520014 Warning: pressure scaling more than 1%, mu: 1.01087 1.01087 1.01087 Step 520014 Warning: pressure scaling more than 1%, mu: 1.01087 1.01087 1.01087 step 520100, will finish Thu Nov 24 07:53:42 2011 step 520200, will finish Thu Nov 24 07:53:42 2011” ，and at last the warning disapper. does it effect the simulation result? and The evolution of temperature is abnormal. Bodu Bo Du Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 E-mail: 2008d...@gmail.com -- 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] do remd in the npt ensemble:Warning: pressure scaling more than 1%, mu: 333821 333821 333821
dear teacher, when i do remd in the npt ensemble. =md.mdp=== ; Start time and timestep in ps tinit= 0 dt = 0.01 nsteps = 5000 ; For exact run continuation or redoing part of a run ; Temperature coupling Tcoupl = nose-hoover ; Groups to couple separately tc_grps = system ; Time constant (ps) and reference temperature (K) tau_t= 0.3 ref_t= 800 ; Pressure coupling Pcoupl = berendsen pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 0.5 compressibility = 6.5e-5 ref_p= 1.0 ==error step 00, will finish Mon Nov 28 00:11:22 2011 step 100, will finish Mon Nov 28 00:11:19 2011 Step 102 Warning: pressure scaling more than 1%, mu: 333821 333821 333821 Step 102 Warning: pressure scaling more than 1%, mu: 455440 455440 455440 --- Program mdrun_mpi_4.5.5, VERSION 4.5.5 Source code file: smalloc.c, line: 214 Fatal error: Not enough memory. Failed to realloc -5476105916 bytes for grid-nra, grid-nra=0x38ce0 (called from file nsgrid.c, line 483) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- ===command= mpirun n8,8,8,11,11,11,11,2 -np $n_thread /export/software/bin/mdrun_mpi_4.5.5 -multidir ./0/ ./1/ ./2/ ./3/ ./4/ ./5/ ./6/ ./7/ ./8/ ./9/ ./10/ ./11/ ./12/ ./13/ ./14/ ./15/ -replex 50 -nice 0 -s pmma.tpr -o md -c after_md -pd -v log1 how could i do except use the smaller dt or big/small tau_p ? thanks! bodu Bo Du Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 E-mail: 2008d...@gmail.com -- 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] Rv: g_helixorient question
I only just ask for a brief explanation for each file, thanks anyway, the gmx_helixorient.c could be a good solution. Thanks again for your response. De: Mark Abraham mark.abra...@anu.edu.au Para: Discussion list for GROMACS users gmx-users@gromacs.org Enviado: martes 22 de noviembre de 2011 13:00 Asunto: Re: [gmx-users] Rv: g_helixorient question On 22/11/2011 10:41 PM, Javier Romero Garcia wrote: Hi, I'm sorry to insist in my question but if somebody could answer or just to send me some information or place to look for, I will be very thanked. I imagine that these kinds of definitions are discussed in general texts on (computational or experimental) modelling of proteins, so that may be a good place to start with understanding what g_helixorient might be calculating. GROMACS manual does not give any information but the way to use it. Nothing about the contain of files. g_helixorient -h has some very basic information that could help. Otherwise, I'm sure the GROMACS team regret that the documentation is a bit lacking. Please do remember that GROMACS is a volunteer effort. Because our resources are finite, it won't always be able to be what we would all like it to be. The existence of the g_helixorient tool is already rather more than you paid for, too ;-). Do consider using other simulation packages' analysis tool sets - often trajectories can be inter-converted with little fuss. In extremis, please consider reading the code of src/tools/gmx_helixorient.c - but you'll need to be unafraid of the mathematics of 3D rotation! Mark Thanks again. - Mensaje reenviado - De: Javier Romero Garcia kurcol...@yahoo.com Para: gmx-users@gromacs.org gmx-users@gromacs.org Enviado: lunes 21 de noviembre de 2011 10:44 Asunto: g_helixorient question Hello! My name's Javier Romero and I am a PhD student, writting from Barcelona. I am simulating an anphipatic helix of 23 residues, in the interface of a DPPC membrane and water. I am trying to measure the rotation of the helix using the tool g_helixorient. Could be somebody so kind to explain me the meaning of each kind of the files? I mean: - Twist. - Tilt. - Tetha. - Rotation. - Rise. - Radius. - Helixaxis. - Center. - Bending. Thanks in advance. -- 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
