[gmx-users] query regarding Fe4S4
Hello I have generated the individual charges of Fe4S4 cluster with Gaussian programm.I have all the interatomic distances and diherdral.I ahve also generated the .top file of the Fe4S4 cluster with the help of mktop pogramm.Can anybody please suggest how do I generated the .itp file for the Fe4S4 cluster.Do I have to do it manually? Isnt there any other way? Subarna Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] query regarding Fe4S4
subarna thakur wrote: Hello I have generated the individual charges of Fe4S4 cluster with Gaussian programm.I have all the interatomic distances and diherdral.I ahve also generated the .top file of the Fe4S4 cluster with the help of mktop pogramm.Can anybody please suggest how do I generated the .itp file for the Fe4S4 cluster.Do I have to do it manually? Isnt there any other way? See http://oldwiki.gromacs.org/index.php/Exotic_Species You will need a lot more information before you can construct a useful topology - by hand or using a tool. 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/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/mailing_lists/users.php
[gmx-users] installing grace
hi, i am simulating a peptide in lipid bilayer where i've completed the production run. but the problem is that i cant install grace as it requires motiff api. a have installed lesstiff but still when i am going to intall grace its again complaining theat it could not find motiff api. it'll be great to have some suggestions regarding grace and motiff installtion. i am using a red hat enterprise edition linux machine. is there any other software than gace to plot the generated graphical output? Thaking you Shamik Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.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/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/mailing_lists/users.php
Re: [gmx-users] H-Db error
Hi, I want to know, by default g_rms calculates RMSD on which atoms set - backbone, all atoms or c-alphas ? How do i modify these settings ? Regards, Nikhil From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 20 July, 2009 7:35:29 AM Subject: Re: [gmx-users] H-Db error nikhil damle wrote: This is how i have modified the entry as i myself created the parameter file for phosphothreonine. This is normal NH hydrogen n no extra added=directly copied from threonine. So y there is an error msg ? i added this residue in aminoacids.dat file as well. and 2ns line is tab separated. Is there any other formatting to b done ?? TPO 1 1 1 H N -C CA This is error msg i get: (I also checked h_db.c programme but could not get much help abt the error msg) --- All occupancies are one Opening library file /home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.atp Atomtype 1 Reading residue database... (ffG43a1) Opening library file /home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.rtp Residue 97 Sorting it all out... Opening library file /home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.hdb --- Program pdb2gmx, VERSION 4.0.5 Source code file: h_db.c, line: 162 Fatal error: Error reading from file ffG43a1 --- That looks weird. Try spaces, not tabs. What does pdb2gmx -debug -yourflags say? If you have an empty line at the end, try removing 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/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/mailing_lists/users.php See the Web#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.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/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/mailing_lists/users.php
[gmx-users] problem with 53a6 simulating a coiled-coil fiber like protein
Dear all I recently performed MD simulations using 53A6 force field with Gromacs4.0 The system includes a protein+water and ions for neutralizing, The protocol is quite classical: NPT ensemble, 300K and reaction field for electrostatics, 2fs for integration, bond lengths are constrained. The protein is a coiled-coil fiber like protein, including different repeat units. At the starting point, the protein roughly adopts a cylinder shape. After few ns ( less than 5), some helices are broken, even unfold. Finally, the protein is kinked,with a kink angle ~ 90°. I tested different constructions but observed similar results. The same system was simulated with NAMD, charmm force field, the structure remains stable all along the simulation (10ns for now ). Did anyone obtain similar results for a coiled coil system with 53A6 force field? here is my .mdp file : nstvout = 1 nstfout = 0 nstxtcout = 2500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist = 5 rlist = 0.8 coulombtype = generalized-reaction-field rcoulomb= 1.4 rvdw= 1.4 epsilon_rf = 62.0 ; Temperature coupling is on in two groups Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein SOL NA+ ; Pressure coupling is not on Pcoupl = Berendsen tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 Thanks a lot for your answers.___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: installing grace
In what way do you install this software: from source or from packages? Do you have the appropriate variable telling the grace where the lesstiff is installed? If you install lesstiff from the package it should have a name like lesstiff-dev (not just lesstiff). ~ Vitaly -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === hi, i am simulating a peptide in lipid bilayer where i've completed the production run. but the problem is that i cant install grace as it requires motiff api. a have installed lesstiff but still when i am going to intall grace its again complaining theat it could not find motiff api. it'll be great to have some suggestions regarding grace and motiff installtion. i am using a red hat enterprise edition linux machine. is there any other software than gace to plot the generated graphical output? Thaking you Shamik ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] installing grace
Quoting Samik Bhattacharya samikb...@yahoo.co.in: hi, i am simulating a peptide in lipid bilayer where i've completed the production run. but the problem is that i cant install grace as it requires motiff api. a have installed lesstiff but still when i am going to intall grace its again complaining theat it could not find motiff api. it'll be great to have some suggestions regarding grace and motiff installtion. i am using a red hat enterprise edition linux machine. is there any other software than gace to plot the generated graphical output? Thaking you Shamik Enable the Fedora EPEL repo http://www.fedoraproject.org/wiki/EPEL/FAQ#howtouse and install grace with # yum -y install grace -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] g_rms (was H-Db error)
If you are changing the topic, please start a new thread to avoid confusion in the archive. When running g_rms, you choose the group for analysis; there is no default. -Justin nikhil damle wrote: Hi, I want to know, by default g_rms calculates RMSD on which atoms set - backbone, all atoms or c-alphas ? How do i modify these settings ? Regards, Nikhil *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Monday, 20 July, 2009 7:35:29 AM *Subject:* Re: [gmx-users] H-Db error nikhil damle wrote: This is how i have modified the entry as i myself created the parameter file for phosphothreonine. This is normal NH hydrogen n no extra added=directly copied from threonine. So y there is an error msg ? i added this residue in aminoacids.dat file as well. and 2ns line is tab separated. Is there any other formatting to b done ?? TPO1 1 1 H N -C CA This is error msg i get: (I also checked h_db.c programme but could not get much help abt the error msg) --- All occupancies are one Opening library file /home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.atp Atomtype 1 Reading residue database... (ffG43a1) Opening library file /home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.rtp Residue 97 Sorting it all out... Opening library file /home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.hdb --- Program pdb2gmx, VERSION 4.0.5 Source code file: h_db.c, line: 162 Fatal error: Error reading from file ffG43a1 --- That looks weird. Try spaces, not tabs. What does pdb2gmx -debug -yourflags say? If you have an empty line at the end, try removing it. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Love Cricket? Check out live scores, photos, video highlights and more. Click here http://in.rd.yahoo.com/tagline_cricket_2/*http://cricket.yahoo.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/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
[gmx-users] A small gift for you.
Hey Discussion,Click below or paste this into your browser:http://youmint.com/network-bhanu_seniya Make money every time Advertisers send you email or SMS.You have received this email because two of your friends have invited you. If you do not wish to receive any further notiications, Decline . Copyright 2007-2008 YouMint Media (P) Ltd. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: installing grace
Hello Shamik, Why not to try from rpm packages? It should be easier especially if this is the fisrt time of doint that. ~ Vitaly -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === On Mon, Jul 20, 2009 at 3:51 PM, Samik Bhattacharya samikb...@yahoo.co.inwrote: --- On *Mon, 20/7/09, Vitaly V. Chaban vvcha...@gmail.com* wrote: From: Vitaly V. Chaban vvcha...@gmail.com Subject: Re: installing grace To: gmx-users@gromacs.org, Samik Bhattacharya samikb...@yahoo.co.in Date: Monday, 20 July, 2009, 4:28 PM In what way do you install this software: from source or from packages? Do you have the appropriate variable telling the grace where the lesstiff is installed? If you install lesstiff from the package it should have a name like lesstiff-dev (not just lesstiff). ~ Vitaly hi, thank you for the answar. i should have mentioned it that i'm installing it from source. no i've not set any variables. i have just used ./configure which alarms me about the absence of Motif api and exits. if i am commiting some mistakes please let me know it. it'll be very helpful if you kindly point out the mistakes or tell the appropiate commands for installing lesstiff and grace. thanking you Shamik -- Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/ . ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Groups based on distance criteria
Hi all I would like to extract the interaction energy between a protein and the solvent within a certain distance from the protein. Is it possible to define a group based on a distance criteria from the protein? I have not found any such feature unfortunately. Any other way of accomplish this? Thank you! Matteus Lindgren - Matteus Lindgren, graduate student Department of Chemistry, Umeå University SE-901 87 Umeå, Sweden Phone: +46 (0)90-7865368 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: Groups based on distance criteria
Hi Matteus, Yeah, dynamic groups would be a powerfull tool. But such mechanism is still under development if I am not out-of-time. The possible way to proceed with such kind of research (as Berk advised me here long ago) is to sort the trajectory (trjorder) based on the distance criteria. Then you can make an index file with N first numbers (which are close to the protein) and use g_energy with this group and protein group. It seems for your task this way is a perfect solution. Please also search the list archive for the details (about a year ago, maybe a bit more). ~ Vitaly -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University, Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === I would like to extract the interaction energy between a protein and the solvent within a certain distance from the protein. Is it possible to define a group based on a distance criteria from the protein? I have not found any such feature unfortunately. Any other way of accomplish this? Thank you! Matteus Lindgren - Matteus Lindgren, graduate student Department of Chemistry, Umeå University SE-901 87 Umeå, Sweden Phone: +46 (0)90-7865368 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Re: Groups based on distance criteria
2009/7/20 Vitaly V. Chaban vvcha...@gmail.com Hi Matteus, Yeah, dynamic groups would be a powerfull tool. But such mechanism is still under development if I am not out-of-time. The possible way to proceed with such kind of research (as Berk advised me here long ago) is to sort the trajectory (trjorder) based on the distance criteria. Then you can make an index file with N first numbers (which are close to the protein) and use g_energy with this group and protein group. It seems for your task this way is a perfect solution. Or better yet, use mdrun -rerun on your reordered trajectory and _then_ use g_energy? This way you would be free of any problems with molecules going in and out of your solvation shell, if I am getting things right. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Some questions on Tabulated Dihedral Potential
Dear all, I tried to include 2 tabulated dihedral potential functions into my simulation. But it seems to be not able to generate correct results. The system just exploded. I defined 3601 points in each table (from -180 to 180 with an increment 0.1). After 'mdrun', GOMACS generates two warning information: WARNING: For the 3598 non-zero entries for table 0 in table_d1.xvg the forces deviate on average 193% from minus the numerical derivative of the potential WARNING: For the 3598 non-zero entries for table 0 in table_d2.xvg the forces deviate on average 193% from minus the numerical derivative of the potential Do these two warnings matter very much? I checked the values for x,f(x),-f'(x) in the tables and don't think there're mistakes. has anyone of you met with such problems? There're also some other confusions: 1. Can the constant k before the cubic spline function be defined arbitrarily, as long as the multiplication of k and f(x) equals to the dihedral potential? 2. The tables do not need to be supplied to mdrun using '-tableb', right? I found if I omitted -tableb and the following table files, GROMACS can still go and find the two tables. 3. how to use '-tableb' if two tables are supplied? '-tableb table_d1.xvg table_d2.xvg' or '-tableb table_d1.xvg -tableb table_d2.xvg'? I tried both and error information was given that GROMACS can not find 'table_d1_d1.xvg'. I then delete '_d1' in both of the commands and there was no error information any more. It seems that only one table can be supplied to mdrun by using'-tableb', the second table can not be recognized all the time. Thanks for your help CH ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.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/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/mailing_lists/users.php
Re: [gmx-users] Re: Groups based on distance criteria
Hi Vasya, Glad to hear from you here! I did not work with -rerun yet - it's a useful option I see now. On Mon, Jul 20, 2009 at 5:39 PM, Vasilii Artyukhov darth.va...@gmail.comwrote: 2009/7/20 Vitaly V. Chaban vvcha...@gmail.com Hi Matteus, Yeah, dynamic groups would be a powerfull tool. But such mechanism is still under development if I am not out-of-time. The possible way to proceed with such kind of research (as Berk advised me here long ago) is to sort the trajectory (trjorder) based on the distance criteria. Then you can make an index file with N first numbers (which are close to the protein) and use g_energy with this group and protein group. It seems for your task this way is a perfect solution. Or better yet, use mdrun -rerun on your reordered trajectory and _then_ use g_energy? This way you would be free of any problems with molecules going in and out of your solvation shell, if I am getting things right. -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] problem with 53a6 simulating a coiled-coil fiber like protein
Well, not coiled coil, but I have observed serious distortions in a all-helix protein with G53A6 and reaction field. Using PME solved the problem. Marcos On Mon, 2009-07-20 at 13:50 +0200, Lory Montout wrote: Dear all I recently performed MD simulations using 53A6 force field with Gromacs4.0 The system includes a protein+water and ions for neutralizing, The protocol is quite classical: NPT ensemble, 300K and reaction field for electrostatics, 2fs for integration, bond lengths are constrained. The protein is a coiled-coil fiber like protein, including different repeat units. At the starting point, the protein roughly adopts a cylinder shape. After few ns ( less than 5), some helices are broken, even unfold. Finally, the protein is kinked,with a kink angle ~ 90°. I tested different constructions but observed similar results. The same system was simulated with NAMD, charmm force field, the structure remains stable all along the simulation (10ns for now ). Did anyone obtain similar results for a coiled coil system with 53A6 force field? here is my .mdp file : nstvout = 1 nstfout = 0 nstxtcout = 2500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist = 5 rlist = 0.8 coulombtype = generalized-reaction-field rcoulomb= 1.4 rvdw= 1.4 epsilon_rf = 62.0 ; Temperature coupling is on in two groups Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein SOL NA+ ; Pressure coupling is not on Pcoupl = Berendsen tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 Thanks a lot for your answers.___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] problem with 53a6 simulating a coiled-coil fiber like protein
marcos wrote: Well, not coiled coil, but I have observed serious distortions in a all-helix protein with G53A6 and reaction field. Using PME solved the problem. Indeed. rlist = 0.8 and any kind of electostatic cut-off was acceptable in about the 1980s :-) Mark Marcos On Mon, 2009-07-20 at 13:50 +0200, Lory Montout wrote: Dear all I recently performed MD simulations using 53A6 force field with Gromacs4.0 The system includes a protein+water and ions for neutralizing, The protocol is quite classical: NPT ensemble, 300K and reaction field for electrostatics, 2fs for integration, bond lengths are constrained. The protein is a coiled-coil fiber like protein, including different repeat units. At the starting point, the protein roughly adopts a cylinder shape. After few ns ( less than 5), some helices are broken, even unfold. Finally, the protein is kinked,with a kink angle ~ 90°. I tested different constructions but observed similar results. The same system was simulated with NAMD, charmm force field, the structure remains stable all along the simulation (10ns for now ). Did anyone obtain similar results for a coiled coil system with 53A6 force field? here is my .mdp file : nstvout = 1 nstfout = 0 nstxtcout = 2500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist = 5 rlist = 0.8 coulombtype = generalized-reaction-field rcoulomb= 1.4 rvdw= 1.4 epsilon_rf = 62.0 ; Temperature coupling is on in two groups Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein SOL NA+ ; Pressure coupling is not on Pcoupl = Berendsen tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 Thanks a lot for your answers.___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] mdrun -nosum still complains that 15 % of the run time was spent communicating energies
Hello,
I have been running simulations on a larger number of processors
recently and am confused about the message regarding -nosum that occurs
at the end of the .log file. In this case, I have included the -nosum
option to mdrun and I still get this warning (gromacs 4.0.4).
My command was:
mpirun -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') -machinefile
$PBS_NODEFILE /scratch/cneale/exe/intel/gromacs-4.0.4/exec/bin/mdrun
-deffnm test -nosum -npme 128
#
To confirm that I am asking mdrun for -nosum, to stderr I get:
...
Option Type Value Description
--
-[no]h bool no Print help info and quit
-niceint0 Set the nicelevel
-deffnm string testSet the default filename for all file options
-[no]xvgrbool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-npmeint128 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or
cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions
with
DD (nm), 0 is determine from initial coordinates
-rconreal 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum autoDynamic load balancing (with DD): auto, no
or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-[no]sum bool no Sum the energies at every step
-[no]v bool no Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]append bool no Append to previous output files when continuing
from checkpoint
-[no]addpart bool yes Add the simulation part number to all output
files when continuing from checkpoint
-maxhreal -1 Terminate after 0.99 times this time (hours)
-multi int0 Do multiple simulations in parallel
-replex int0 Attempt replica exchange every # steps
-reseed int-1 Seed for replica exchange, -1 is generate a seed
-[no]glasbool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
...
And the message at the end of the .log file is:
...
D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
av. #atoms communicated per step for force: 2 x 3376415.3
av. #atoms communicated per step for LINCS: 2 x 192096.6
Average load imbalance: 11.7 %
Part of the total run time spent waiting due to load imbalance: 7.9 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds:
X 0 % Y 0 % Z 0 %
Average PME mesh/force load: 0.620
Part of the total run time spent waiting due to PP/PME imbalance: 10.0 %
NOTE: 7.9 % performance was lost due to load imbalance
in the domain decomposition.
NOTE: 10.0 % performance was lost because the PME nodes
had less work to do than the PP nodes.
You might want to decrease the number of PME nodes
or decrease the cut-off and the grid spacing.
R E A L C Y C L E A N D T I M E A C C O U N T I N G
Computing: Nodes Number G-CyclesSeconds %
---
Domain decomp. 256 51 337.551 131.2 0.7
Send X to PME256501 59.454 23.1 0.1
Comm. coord. 256501 289.936 112.7 0.6
Neighbor search 256 51 1250.088 485.9 2.8
Force25650116105.584 6259.935.4
Wait + Comm. F 256501 2441.390 948.9 5.4
PME mesh 128501 5552.336 2158.112.2
Wait + Comm. X/F 128501 9586.486 3726.121.1
Wait + Recv. PME F 256501 459.752 178.7 1.0
Write traj. 256 2 223.993 87.1 0.5
Update 256501 777.618 302.2 1.7
Constraints 256 1002 1223.093 475.4 2.7
Comm. energies 256 51 7011.309 2725.115.4
Rest
Re: [gmx-users] Peptide - DMPC membrane simulations - Unstable system
I think I have not arrived to complete solution of my problem yet, but I think the cause of early LINCS warnings were version incompatibility. I am now trying to run simulation on the server that has only 4.0.5 Gromacs, will see if that helps and whether I will warnings in the middle of simulations. I have tried PR simulation on peptide and it failed even earlier (after 10,000 steps), maybe this indicates version issues, as I would assume PR simulations are more stable as they does not allow peptide to enter DMPC layer So after 20 ns of simulation on the server with Gromacs 4.0 I've started to get errors and LINCS warnings and simulation collapsed, I have resumed simualtion as per oldwiki instructions, but again it soon failed. After looking at the trajectory with VMD I see that the peptide sinks into DMPC and one phenyl ring flips out (Phe residue). Maybe due to local constrains and being surrounded by DMPC the errors start coming up. I am not sure. I will do the movie and post it on youtube as ato show you what is going on. Why does the system fails after 10,578,600 steps? Is there way to ignore LINCS warnings and make simulation run anyways, if yes how? I was not sure what to try next. Try to do several EM steps to get system to 500 kJ/mol, right now it is at 800 kJ/mol? Or try to do longer equilibration steps by restraining protein using posre.itp file included in topology as per your tutorial? Thanks for your time. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] parameters for Phosphorylated threonine and serine
I also cannot open the ffg43a1p file, using the mozilla firefox download manager, on Ubuntu Jaunty. Some months ago I could open it in Windows. Mensaje citado por Justin A. Lemkul jalem...@vt.edu: nikhil damle wrote: *.tar gives error during extracting saying that it is not a .tar archive. Works fine for me. What are you doing to try to open it? -Justin Regards, Nikhil *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, 18 July, 2009 9:31:01 PM *Subject:* Re: [gmx-users] parameters for Phosphorylated threonine and serine nikhil damle wrote: Hi, Can anyone suggest me where to get phosphorylated ser and threonine parameters ? The ffG43a1p tarball is available under User Contributions on the Gromacs website: http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Force_fields As I recall, there were some formatting problems with some of the files (they were made under a very old Gromacs version, and some formatting has since changed). If you run into problems, you may contact me off-list; I should have the corrected files. -Justin Regards, Nikhil Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8 http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/. ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8 http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: mdrun -nosum still complains that 15 % of the run time was spent communicating energies
I have now tested with and without -nosum and it appears that the option
is working (see 51 vs. 501 Number of communications) but that the total
amount of time communicating energies didn't go down by very much. Seems
strange to me. Anybody have any ideas if this is normal?
At the very least, I suggest adding an if statement to mdrun so that it
doesn't output the -nosum usage note if the user did in fact use -nosum
in that run.
Without using -nosum:
R E A L C Y C L E A N D T I M E A C C O U N T I N G
Computing: Nodes Number G-CyclesSeconds %
---
...
Write traj. 256 2 233.218 93.7 0.5
Update 256501 777.511 312.5 1.7
Constraints 256 1002 1203.894 483.9 2.7
Comm. energies 256501 7397.995 2973.916.5
Rest 256 128.058 51.5 0.3
---
Total384 44897.46818048.0 100.0
---
NOTE: 16 % of the run time was spent communicating energies,
you might want to use the -nosum option of mdrun
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 47.000 47.000100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 13485.788712.634 1.842 13.029
Finished mdrun on node 0 Mon Jul 20 12:53:41 2009
#
And using -nosum:
R E A L C Y C L E A N D T I M E A C C O U N T I N G
Computing: Nodes Number G-CyclesSeconds %
---
...
Write traj. 256 2 213.521 83.3 0.5
Update 256501 776.606 303.0 1.8
Constraints 256 1002 1200.285 468.2 2.7
Comm. energies 256 51 6926.667 2702.115.6
Rest 256 127.503 49.7 0.3
---
Total384 44296.67017280.0 100.0
---
NOTE: 16 % of the run time was spent communicating energies,
you might want to use the -nosum option of mdrun
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 45.000 45.000100.0
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 14084.547744.277 1.924 12.475
#
Thanks,
Chris.
Chris Neale wrote:
Hello,
I have been running simulations on a larger number of processors
recently and am confused about the message regarding -nosum that
occurs at the end of the .log file. In this case, I have included the
-nosum option to mdrun and I still get this warning (gromacs 4.0.4).
My command was:
mpirun -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') -machinefile
$PBS_NODEFILE /scratch/cneale/exe/intel/gromacs-4.0.4/exec/bin/mdrun
-deffnm test -nosum -npme 128
#
To confirm that I am asking mdrun for -nosum, to stderr I get:
...
Option Type Value Description
--
-[no]h bool no Print help info and quit
-niceint0 Set the nicelevel
-deffnm string testSet the default filename for all file options
-[no]xvgrbool yes Add specific codes (legends etc.) in the
output
xvg files for the xmgrace program
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-npmeint128 Number of separate nodes to be used for
PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or
cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded
interactions with
DD (nm), 0 is determine from initial
coordinates
-rconreal 0 Maximum distance for P-LINCS (nm), 0 is
estimate
-dlb enum autoDynamic load balancing (with DD): auto, no
or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell
size
-[no]sum bool no Sum the energies at every step
-[no]v bool no Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid
[gmx-users] append option does not work when the traj.trr is larger than 2GB (v4.0.5)
Hello, I'm having a problem in continuing a simulation with append flag once traj.trr file is larger than 2GB. I reported this issue before when I was using gromacs version 4.0.4 (please check the following link) http://bugzilla.gromacs.org/show_bug.cgi?id=315 The problem still exists in version 4.0.5 and the append flag works only at version 4.0.2. I've tested not only various distributions of linux but also different remote and local machines and concluded that it's not the problem of special systems but a kind of major bug. I hope that anyone who had the same experience can share some information about this issue. Anyone interested in understanding or debugging this bug can download the input files to reproduce the problem from the above link. Any advice or information would be greatly appreciated. Thank you Kyungchan ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
