Re: [gmx-users] Re: Simulation in the high temperature conditions
Dear Gromacs Users! By that moments I've completed 2 sets of simulation in high temperature 1- With applied posres on the backbone atoms ( fc= 200 ). The result was- that the posres prevented motion of the helixes as the rigid bodies so I've not noticed any conformation sampling. Question : Could I observe some conformation sampling on that trajectory by means of some external tricks ? E.g extracting of the eigenvectors via PCA? 2 With applied network of disres applied on backbone atoms of the helix elements of my protein within Rc=1nm. As the result of that simulation I've observed distortion of my protein wich resulted in some kind of shrinking of the helix elements. Question : How I could specify that disres more correctly ? If I've observed some kind of shrinking of my protein does it means that Rc was chosen incorectly or should I define disres in anothe manner ? ( I'have not quite understand what exatly is the R_fract and in what situation it could be useful ). James -- 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] Clustering
Hi, It's been a while since I used g_clustsize, but if I'm not mistaken you get the number of molecules per cluster as output, from which you can estimate the physical size of the clusters with a few assumptions. If that's not good enough you also get the identities of the molecules in the clusters, which you can then use as input, along with the trajectory, for g_gyrate (or similar) to get more information. trjconv -cluster doesn't calculate the sizes or report anything new, so I find it mostly useful for visualization in this context. Best, Erik 15 apr 2012 kl. 12.02 skrev dina dusti: Dear Erik, Thank you very much from your response, but I want to calculate the radius of these cluster. I want to know that I should do clustering with trjconv -cluster similar with micelle clustering and then calculate the radius of these? Best Regards Dina From: Erik Marklund er...@xray.bmc.uu.se To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 15, 2012 12:58 PM Subject: Re: [gmx-users] Clustering Try g_clustsize Erik 15 apr 2012 kl. 09.00 skrev dina dusti: Dear GROMACS Specialists, May I know about clustering, Please? I want cluster small organic molecules. Is it possible? They collected in some places together and they are separate in the other place. Please help me. Thank you very much in advance. Best Regards Dina -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.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] Re:Data Analysis
Dear All, Is there a way to extract the pull force (and not the total force or energy) for a specified group (indexed) or center of mass, rather than just the total pullf over a run? I wanted to break up the pullf into varied sub contributions, however as it is applied to the center of mass of the pull group, I do not know if it is possible. I am just trying to sort out easier Vs. More complicated means of doing the same thing as there are several methods for achieving the end result I wanted (output plots). Any suggestions are appriciated as well. Sincerely, Stephan Lloyd Watkins -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- 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] Fe atom problems....in simulation
CAn any one siggest me how can I run simulation a protein containing Fe atom, I have changed the iions.itpfile and included there Fe in residue type.dat bu still it is returning an error. FE parameter not found. -- 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] Fe atom problems....in simulation
Hi, You have to had LJ parameters in ffnonbonded.itp file in the subfolder relative to your force-field Francesco Il giorno 16 aprile 2012 11:08, Kamalesh Roy roy.kamales...@gmail.com ha scritto: CAn any one siggest me how can I run simulation a protein containing Fe atom, I have changed the iions.itpfile and included there Fe in residue type.dat bu still it is returning an error. FE parameter not found. -- 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 -- Cordiali saluti, Dr.Oteri 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] DD load balancing is limited by minimum cell size in dimension Z
Hi all What does the following note mean in the log file DD load balancing is limited by minimum cell size in dimension Z Is is purely a performance related issue ? Cheers Gavin -- 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: Simulation in the high temperature conditions
James Starlight wrote: Dear Gromacs Users! By that moments I've completed 2 sets of simulation in high temperature 1- With applied posres on the backbone atoms ( fc= 200 ). The result was- that the posres prevented motion of the helixes as the rigid bodies so I've not noticed any conformation sampling. Question : Could I observe some conformation sampling on that trajectory by means of some external tricks ? E.g extracting of the eigenvectors via PCA? If you've restrained the position of the atoms, there's no trick that can magically give you a more desirable result. You've limited the ability of atoms to move, plain and simple. 2 With applied network of disres applied on backbone atoms of the helix elements of my protein within Rc=1nm. What does Rc mean here? As the result of that simulation I've observed distortion of my protein wich resulted in some kind of shrinking of the helix elements. Question : How I could specify that disres more correctly ? If I've observed some kind of shrinking of my protein does it means that Rc was chosen incorectly or should I define disres in anothe manner ? ( I'have not quite understand what exatly is the R_fract and in what situation it could be useful ). Without seeing your [distance_restraints] directive, it's impossible to comment aside from saying that if your structure distorted severely, then yes, you did something wrong. I also don't know what R_fract is. -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
[gmx-users] how to install DSSP in linux with Gromacs 4.0.7
Hi:I am getting upsep to install DSSP in linux with Gromacs 4.0.7I do not know where is the problemwhich DSSP file I should download itand possible because gromacs 4.0.7 ?could someone can help me to figure out it ?many thanks Best Wishesli-hua -- 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 install DSSP in linux with Gromacs 4.0.7
李 麗花 wrote: Hi: I am getting upsep to install DSSP in linux with Gromacs 4.0.7 I do not know where is the problem which DSSP file I should download it and possible because gromacs 4.0.7 ? could someone can help me to figure out it ? many thanks http://swift.cmbi.ru.nl/gv/dssp/ Under Miscellaneous, click Distribution and you will find the DSSPold executables, which are the old version of DSSP that are compatible with Gromacs. -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
[gmx-users] Clustering
Hi Erik, Thank you very much from your response. Best Regards Dina From: Erik Marklund er...@xray.bmc.uu.se To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, April 16, 2012 12:07 PM Subject: Re: [gmx-users] Clustering Hi, It's been a while since I used g_clustsize, but if I'm not mistaken you get the number of molecules per cluster as output, from which you can estimate the physical size of the clusters with a few assumptions. If that's not good enough you also get the identities of the molecules in the clusters, which you can then use as input, along with the trajectory, for g_gyrate (or similar) to get more information. trjconv -cluster doesn't calculate the sizes or report anything new, so I find it mostly useful for visualization in this context. Best, Erik 15 apr 2012 kl. 12.02 skrev dina dusti: Dear Erik, Thank you very much from your response, but I want to calculate the radius of these cluster. I want to know that I should do clustering with trjconv -cluster similar with micelle clustering and then calculate the radius of these? Best Regards Dina From: Erik Marklund er...@xray.bmc.uu.se To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 15, 2012 12:58 PM Subject: Re: [gmx-users] Clustering Try g_clustsize Erik 15 apr 2012 kl. 09.00 skrev dina dusti: Dear GROMACS Specialists, May I know about clustering, Please? I want cluster small organic molecules. Is it possible? They collected in some places together and they are separate in the other place. Please help me. Thank you very much in advance. Best Regards Dina -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.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
Re: [gmx-users] DD load balancing is limited by minimum cell size in dimension Z
On 16/04/2012 8:43 PM, Gavin Melaugh wrote: Hi all What does the following note mean in the log file DD load balancing is limited by minimum cell size in dimension Z Is is purely a performance related issue ? Yes. See 3.17.2 for description of DLB. Various algorithms constrain minimum cell sizes. Perhaps due to inhomogeneous particle distribution, ideal load balance would require violation of the minimum size. So GROMACS does the correct thing - compromises load balance (and thus performance) and lets you know there's an issue. 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: Simulation in the high temperature conditions
Justin, I've applied disres on each backbone atom of my potein within cutoff distance of 1nm ( Rc=1.0 nm). I've selected this value for cutoff to decrease overall ammount of the restains in my itp file. Also such value ( 1nm) was selected because of the relatively tight packing of the alpha helices in the TM buddle of membrane protein. The selected values for disre_dist, disre_up2 and disre_frac were 1, 1.2 and 0.5 nm respectually . Also I've made disres with 1 and 0 nm values but I have not noticed any difference in the resulted behaviour of the constrained system. As the consequence I have not clearly realise what exactly is the disre_frac and in what exactly cases this option could be helpfull. This is an example of my output itp file [ distance_restraints ] ; i j ? label funct loup1up2 weight 1 5 1 0 1 01.647312.64731 1 110 1 1 1 0 1.7326 2.7326 1 112 1 2 1 01.838862.83886 1 114 1 3 1 01.960792.96079 1 115 1 4 1 02.035033.03503 1 117 1 5 1 01.990072.99007 1 119 1 6 1 02.088793.08879 1 127 1 7 1 02.139163.13916 1 129 1 8 1 02.271473.27147 1 130 1 9 1 02.357933.35793 1 I've made 10 ns simulation of such system and observe rapid shrinking of my protein starting with first 100ps like the distances that I chose were too small and forces shrink my protein. But when I've tried larger distance value for disre_dist my protein denatured rapidly as no disres were presented. So the main question is How I could specify this disre values if I want to restrain the motion of the helixes of my protein within disre value ( e.g 10 A) relatively current confrmation ? James 16 апреля 2012 г. 15:05 пользователь Justin A. Lemkul jalem...@vt.eduнаписал: James Starlight wrote: Dear Gromacs Users! By that moments I've completed 2 sets of simulation in high temperature 1- With applied posres on the backbone atoms ( fc= 200 ). The result was- that the posres prevented motion of the helixes as the rigid bodies so I've not noticed any conformation sampling. Question : Could I observe some conformation sampling on that trajectory by means of some external tricks ? E.g extracting of the eigenvectors via PCA? If you've restrained the position of the atoms, there's no trick that can magically give you a more desirable result. You've limited the ability of atoms to move, plain and simple. 2 With applied network of disres applied on backbone atoms of the helix elements of my protein within Rc=1nm. What does Rc mean here? As the result of that simulation I've observed distortion of my protein wich resulted in some kind of shrinking of the helix elements. Question : How I could specify that disres more correctly ? If I've observed some kind of shrinking of my protein does it means that Rc was chosen incorectly or should I define disres in anothe manner ? ( I'have not quite understand what exatly is the R_fract and in what situation it could be useful ). Without seeing your [distance_restraints] directive, it's impossible to comment aside from saying that if your structure distorted severely, then yes, you did something wrong. I also don't know what R_fract is. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Atom MNZ1 in residue LYS 107 was not found
Dear Gmx Users, I run implicit simulation for 1 us with virtual sites on hydrogens, then using VMD extracted coordinates into the pdb file. As I want to run explicit solvent simulation now I removed hydrogens so that pdb2gmx will add them. Then I got an error while trying to pdb2gmx using Charmm27: Atom MNZ1 in residue LYS 107 was not found in rtp entry LYS with 22 atoms while sorting atoms. How come this atom appears in my pdb file? Any suggestions? Thank you, Steven -- 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: pre-wham
Dear all, Im using wham on series of runs and have run into the following proble. The command line g_wham_d -if pullf.dat -it tpr.dat -temp 300 -o whamf.xvg -hist outf.hist -unit kCal will work in one run, but not the next one as I go through I found a couple that give the error Fatal error: Found 1 pull groups in traj_4.tpr, but 2 data columns in pullf.xvg (expected 1) if I remove the time column, then it asks for two columns. I get the same thing from the pullx. now, I have looked and looked and can not find a problem in anything. All the .tpr files were generated from a template file the same, all the outputs look the same and have the same format and positions down to tab spacing, and the input files (Dat files) are simple one lines pullf.xvg, pullx.xvg or #.tpr. This one is driving me batty as I cant find an inconsistency but have an inconsitent error message. This is around only a couple runs, and I was going over each one individually with wham, before the generalized mass submission to wham for error bars and gaussien. The ones that work give nice curves and are relativly close in output, the pullf and pullx of the ones that work and dont are realitve as well? Any suggestions before I go batty are appriciated. Sincerely, Stephan Watkins An example pullf or pull x file @title Pull COM @xaxis label Time (ps) @yaxis label Position (nm) @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 0 Y @ s1 legend 1 dY 0. 5.46393 5.31908 2. 5.47052 5.34938 4. 5.46465 5.3283 6. 5.46107 5.3163 8. 5.46298 5.31637 ... or # # mdrun_mpi_d is part of G R O M A C S: # # GROningen MAchine for Chemical Simulation # @title Pull force @xaxis label Time (ps) @yaxis label Force (kJ/mol/nm) @TYPE xy 0. -7.99361e-11 2. 58.602 4. 14.4378 6. 11.5715 8. 13.4292 10. 31.9026 12. 28.7603 14. 25.9416 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- 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: Simulation in the high temperature conditions
James Starlight wrote: Justin, I've applied disres on each backbone atom of my potein within cutoff distance of 1nm ( Rc=1.0 nm). I've selected this value for cutoff to decrease overall ammount of the restains in my itp file. Also such value ( 1nm) was selected because of the relatively tight packing of the alpha helices in the TM buddle of membrane protein. I still don't see how you're defining this cutoff anywhere in genrestr or any other step. Do you have some special index group that you're using in your genrestr command? It may not be relevant, I'm just very confused. The selected values for disre_dist, disre_up2 and disre_frac were 1, 1.2 and 0.5 nm respectually . Also I've made disres with 1 and 0 nm values but I have not noticed any difference in the resulted behaviour of the constrained system. As the consequence I have not clearly realise what exactly is the disre_frac and in what exactly cases this option could be helpfull. The -disre_dist option sets the tolerance for defining the 'lo' value. By default, it is a fixed distance below the actual distance contained in the coordinate file. The default value is 0.1, so if your distance is 0.5, the 'lo' value is set to 0.4 (i.e. 0.5 - 0.1). When using the -disre_frac value, the value specified in -disre_dist is ignored, so be aware that when you combine the two, you override -disre_dist (as stated in genrestr -h). So if you're using -disre_frac of 0.5, your 'lo' value for a 0.5-nm distance is 0.25. This is an example of my output itp file [ distance_restraints ] ; i j ? label funct loup1up2 weight 1 5 1 0 1 01.647312.64731 1 110 1 1 1 0 1.7326 2.7326 1 112 1 2 1 01.838862.83886 1 114 1 3 1 01.960792.96079 1 115 1 4 1 02.035033.03503 1 117 1 5 1 01.990072.99007 1 119 1 6 1 02.088793.08879 1 127 1 7 1 02.139163.13916 1 129 1 8 1 02.271473.27147 1 130 1 9 1 02.357933.35793 1 I've made 10 ns simulation of such system and observe rapid shrinking of my protein starting with first 100ps like the distances that I chose were too small and forces shrink my protein. But when I've tried larger distance value for disre_dist my protein denatured rapidly as no disres were presented. The problem here is that you're allowing all distances between 0 and 'up1' to experience zero restraining force. That gives the system incredibly wide latitude and basically makes the restraints useless. What you're calling either shrinking or denaturing are likely just two possible outcomes from the structure being destabilized in some way. Try running genrestr with default options to see if you get a better result. So the main question is How I could specify this disre values if I want to restrain the motion of the helixes of my protein within disre value ( e.g 10 A) relatively current confrmation ? Are you wanting the restraints to be maintained within a 1-nm distance of their current value? That's a very wide latitude. If that's what you want, then use the -disre_dist option without -disre_frac. -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] Atom MNZ1 in residue LYS 107 was not found
Sounds like a bad VMD selection that didn't remove MNZ1 when you did the conversion. MNZ1 sounds like a virtual site for the extra hydrogen off NZ in protonated LYS. On 2012-04-16 02:32:09PM +0100, Steven Neumann wrote: Dear Gmx Users, I run implicit simulation for 1 us with virtual sites on hydrogens, then using VMD extracted coordinates into the pdb file. As I want to run explicit solvent simulation now I removed hydrogens so that pdb2gmx will add them. Then I got an error while trying to pdb2gmx using Charmm27: Atom MNZ1 in residue LYS 107 was not found in rtp entry LYS with 22 atoms while sorting atoms. How come this atom appears in my pdb file? Any suggestions? Thank you, Steven -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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: Simulation in the high temperature conditions
Justin, Thank you for explanation. Tomorrow I'll try to check results of simulation with the disres applied with its default values as well as with narrower -disre_dist values ( ignorring -disre_frac option at all ) and post here results of such simulations. 1) The cut-off distance wich I've specified was defined with the genrest comand with the -cutoff 1.0 flag. Finally all restrains were apllied on the backbone atoms of alpha helices of the Transmembrane domain of my protein wich I've defined in the index.ndx file. So all loops of my protein were not-restrained at all. Also I have some small question about size of output edr file. I've noticed that size of this files of such simulations (with the disres applied as well as with the -pd flag ) is a very big ( 10-15 gb) Why this occurs and how I could fix it? thanks again for help, James 16 апреля 2012 г. 17:36 пользователь Justin A. Lemkul jalem...@vt.eduнаписал: James Starlight wrote: Justin, I've applied disres on each backbone atom of my potein within cutoff distance of 1nm ( Rc=1.0 nm). I've selected this value for cutoff to decrease overall ammount of the restains in my itp file. Also such value ( 1nm) was selected because of the relatively tight packing of the alpha helices in the TM buddle of membrane protein. I still don't see how you're defining this cutoff anywhere in genrestr or any other step. Do you have some special index group that you're using in your genrestr command? It may not be relevant, I'm just very confused. The selected values for disre_dist, disre_up2 and disre_frac were 1, 1.2 and 0.5 nm respectually . Also I've made disres with 1 and 0 nm values but I have not noticed any difference in the resulted behaviour of the constrained system. As the consequence I have not clearly realise what exactly is the disre_frac and in what exactly cases this option could be helpfull. The -disre_dist option sets the tolerance for defining the 'lo' value. By default, it is a fixed distance below the actual distance contained in the coordinate file. The default value is 0.1, so if your distance is 0.5, the 'lo' value is set to 0.4 (i.e. 0.5 - 0.1). When using the -disre_frac value, the value specified in -disre_dist is ignored, so be aware that when you combine the two, you override -disre_dist (as stated in genrestr -h). So if you're using -disre_frac of 0.5, your 'lo' value for a 0.5-nm distance is 0.25. This is an example of my output itp file [ distance_restraints ] ; i j ? label funct loup1up2 weight 1 5 1 0 1 01.647312.64731 1 110 1 1 1 0 1.7326 2.7326 1 112 1 2 1 01.838862.83886 1 114 1 3 1 01.960792.96079 1 115 1 4 1 02.035033.03503 1 117 1 5 1 01.990072.99007 1 119 1 6 1 02.088793.08879 1 127 1 7 1 02.139163.13916 1 129 1 8 1 02.271473.27147 1 130 1 9 1 02.357933.35793 1 I've made 10 ns simulation of such system and observe rapid shrinking of my protein starting with first 100ps like the distances that I chose were too small and forces shrink my protein. But when I've tried larger distance value for disre_dist my protein denatured rapidly as no disres were presented. The problem here is that you're allowing all distances between 0 and 'up1' to experience zero restraining force. That gives the system incredibly wide latitude and basically makes the restraints useless. What you're calling either shrinking or denaturing are likely just two possible outcomes from the structure being destabilized in some way. Try running genrestr with default options to see if you get a better result. So the main question is How I could specify this disre values if I want to restrain the motion of the helixes of my protein within disre value ( e.g 10 A) relatively current confrmation ? Are you wanting the restraints to be maintained within a 1-nm distance of their current value? That's a very wide latitude. If that's what you want, then use the -disre_dist option without -disre_frac. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] Re: Simulation in the high temperature conditions
James Starlight wrote: Justin, Thank you for explanation. Tomorrow I'll try to check results of simulation with the disres applied with its default values as well as with narrower -disre_dist values ( ignorring -disre_frac option at all ) and post here results of such simulations. 1) The cut-off distance wich I've specified was defined with the genrest comand with the -cutoff 1.0 flag. Finally all restrains were apllied on the backbone atoms of alpha helices of the Transmembrane domain of my protein wich I've defined in the index.ndx file. So all loops of my protein were not-restrained at all. Ah, I see now. Also I have some small question about size of output edr file. I've noticed that size of this files of such simulations (with the disres applied as well as with the -pd flag ) is a very big ( 10-15 gb) Why this occurs and how I could fix it? There are energy terms associated with distance restraints. They cause the .edr file to get large very fast if you have a lot of them. You'll have to decrease nstenergy to make the files smaller, or not use the restraints. -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] Atom MNZ1 in residue LYS 107 was not found
Thankl you. Well... Indeed, just removed them manually and everything is ok. Steven On Mon, Apr 16, 2012 at 2:38 PM, Peter C. Lai p...@uab.edu wrote: Sounds like a bad VMD selection that didn't remove MNZ1 when you did the conversion. MNZ1 sounds like a virtual site for the extra hydrogen off NZ in protonated LYS. On 2012-04-16 02:32:09PM +0100, Steven Neumann wrote: Dear Gmx Users, I run implicit simulation for 1 us with virtual sites on hydrogens, then using VMD extracted coordinates into the pdb file. As I want to run explicit solvent simulation now I removed hydrogens so that pdb2gmx will add them. Then I got an error while trying to pdb2gmx using Charmm27: Atom MNZ1 in residue LYS 107 was not found in rtp entry LYS with 22 atoms while sorting atoms. How come this atom appears in my pdb file? Any suggestions? Thank you, Steven -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- 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 install DSSP in linux with Gromacs 4.0.7
16 apr 2012 kl. 13.32 skrev Justin A. Lemkul: 李 麗花 wrote: Hi: I am getting upsep to install DSSP in linux with Gromacs 4.0.7 I do not know where is the problem which DSSP file I should download it and possible because gromacs 4.0.7 ? could someone can help me to figure out it ? many thanks http://swift.cmbi.ru.nl/gv/dssp/ Under Miscellaneous, click Distribution and you will find the DSSPold executables, which are the old version of DSSP that are compatible with Gromacs. -Justin There's a patch under review that will provide support for DSSP 2.X. Just thought I'd mention it, since there are plenty of questions on the user list regarding do_dssp and this version incompatibility will be resolved in future gromacs releases. Best, Erik -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.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] Protein ligand molecular dynamics simulation
Hi all, I have done complex (protein + ligand) complex from autodock software using this complex im trying to follow http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html tutorial But when i take complex structure directly from autodock result and run PDB2GMX it will give error because it is not recognizing ligand topology which is in complex structure. Then i followed justin tutorial took protein alone and applied Charmm27 Force field and used generate ligand topologies using Swissparam tool ( http://swissparam.ch/) when i do Editconf and created cubic box ligand is going away from protein. Actually my main task to place ligand in paraticular binding site in my protein and perform molecular dynamics. Can any body tell me how to do this..? Thanks in advance -- Sainitin D -- 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] Charmm27.ff with FEP
Hi, Is there any known issue/problem in running FEP calculations with charm27.ff in gromacs4.5.4 ? I tried running an FEP calculation using charmm27.ff by interpolating A state and B state but it gives error that dihedral terms with multiple values can not be interpolated..One need to write all A and B states in topol.top manully. With opls.ff , it does not have any such problem. Any idea? Thanks Sanku-- 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] Charmm27.ff with FEP
On 17/04/2012 1:14 AM, Sanku M wrote: Hi, Is there any known issue/problem in running FEP calculations with charm27.ff in gromacs4.5.4 ? I tried running an FEP calculation using charmm27.ff by interpolating A state and B state but it gives error that dihedral terms with multiple values can not be interpolated..One need to write all A and B states in topol.top manully. With opls.ff , it does not have any such problem. Probably related to type 9 dihedrals, but without copies of the error and relevant parts of your .top file, nobody will be able to say anything. 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] protein and DMPC in Charmm36 ff
An easy way to build a protein in a bilayer is through the charmm-gui website www.charmm-gui.org/ Partial drawbacks are that you need CHARMM to perform final equilibration and then may need to rename some atoms to work with GROMACS On plus side is that charmm36.ff retains the original CHARMM atom names in the lipids Krzysztof Kuczera On 4/15/12 12:09 PM, Tomek Wlodarski wrote: Hi, I would like to simulate protein in DMPC bilayer in Charmm36 ff. I checked mailing list and KALP-15 tutorial, but still I have a few basic questions. 1) I have problem with DMPC bilayer... - VMD membrane builder only provides POPE and POPC lipids... - on the Peter Tieleman page there is a pdb but with different atom names and without H, of course I can rename atoms but pdb2gmx would not regenerate hydrogens - lipids.hdb file is empty - I have found also this page: http://terpconnect.umd.edu/~jbklauda/research/download.html http://terpconnect.umd.edu/%7Ejbklauda/research/download.html and it works but I am not able to extend bilayer with genconf... I always end up with separated copies of starting patch... even with -dist 0 0 0. 2) How to choose proper lipid patch size and simulation box size? For globular proteins I would just run editconf with -bt dodecahedron -d 1. How it is done in membrane protein simulation? Thanks a lot for any help and suggestions. Best! tomek -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.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] NPT simulation for mutation study
Dear Gromcas users, I am doing some mutation study, NPT simulations. Initially I was using a generic .mdp file I got from my advisor and I was able to run the systems for ~50ns with out any issues. But then I spend time reading about gromacs and created a .mdp file. However, with my .mdp file the runs are crashing with error: Fatal error: The X-size of the box (4.500406) times the triclinic skew factor (1.00) is smaller than the number of DD cells (5) times the smallest allowed cell size (0.90) I understand I can try particle decomposition for this system, but before I want to make sure there is no error in my .mdp file. When I load the trajectory in the vmd, I can see the box is getting compressed too much. The contents of the current .mdp file are shown below. This .mdp file varies from my advisor's for few parameters which I have shown at the end. contents of my .mdp file: title= Yo cpp = /usr/bin/cpp include = define = integrator = sd tinit= 0.0 dt = 0.002 nsteps = 5000 nstxout = 100 nstvout = 100 nstfout = 100 nstlog = 1 nstenergy= 1 nstxtcout= 1 xtc_precision= 1000 xtc_grps = energygrps = nstlist = 10 ns_type = grid pbc = xyz rlist= 0.9 domain-decomposition = no coulombtype = PME fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-05 optimize_fft = no epsilon_surface = 0 ewald_geometry = 3d rcoulomb = 0.9 vdwtype = Cut-off rvdw = 0.9 epsilon_r= 1 DispCorr = EnerPres ; with sd as integrator tcoupl is ignored tc-grps = system ; good choice for zeta is 0.5 1/s tau_t= 2.0 ref_t= 310 pcoupl = berendsen pcoupltype = anisotropic nstpcouple = -1 tau_p= 1.0 compressibility = 4.6e-5 4.6e-5 4.6e-5 0 0 0 ref_p= 1.0 1.0 1.0 0.0 0.0 0.0 annealing= no ;annealing_npoints = 3 ;annealing_time = 0 gen_vel = no gen_temp = 310 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS continuation = no lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 morse= no disre= no disre_weighting = equal disre_mixed = no disre_fc = 1000 disre_tau= 10 nstdisreout = 1000 Parameters that are different in my advisor's file: DispCorr = Ener tau_t= 0.20 compressibility = 5e-6 5e-6 5e-6 0 0 0 gen_vel = yes gen_temp = 1 gen_seed = 473529 I thought when using vdw cutoff, it is recommended to use dispersion corrections for both pressure and energy. Also can some explain the reason behind this? For tau_t, I used 2 as it is the recommended value for sd integrator in the manual. Also gen_vel has to be no for sd integrator, correct? Any help will be appreciated! Thanks in advance, Shyno -- Shyno Mathew PhD student Department of Chemical Engineering Columbia University -- 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] GROMOS87 and CHARMM27
Dear GROMACS users, I reproduced the results of a protein-membrane system by using force field GROMOSE87. This protein forms ion channel in membrane. Now if I wanna study the ion conduction through this channel using force field CHARMM27 in umbrella sampling method, is it possible? Can I use the results of the system simulation which has been derived by GROMOS87? Thanks in advance, Shima -- 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] NPT simulation for mutation study
On 2012-04-16 17:23, Shyno Mathew wrote: Dear Gromcas users, I am doing some mutation study, NPT simulations. Initially I was using a generic .mdp file I got from my advisor and I was able to run the systems for ~50ns with out any issues. But then I spend time reading about gromacs and created a .mdp file. However, with my .mdp file the runs are crashing with error: Fatal error: The X-size of the box (4.500406) times the triclinic skew factor (1.00) is smaller than the number of DD cells (5) times the smallest allowed cell size (0.90) use isotropic pressure scaling. if you make mutations, take care to use the same number of water molecules and ions, such that you can compare the energies of the systems. I understand I can try particle decomposition for this system, but before I want to make sure there is no error in my .mdp file. When I load the trajectory in the vmd, I can see the box is getting compressed too much. The contents of the current .mdp file are shown below. This .mdp file varies from my advisor's for few parameters which I have shown at the end. contents of my .mdp file: title= Yo cpp = /usr/bin/cpp include = define = integrator = sd tinit= 0.0 dt = 0.002 nsteps = 5000 nstxout = 100 nstvout = 100 nstfout = 100 nstlog = 1 nstenergy= 1 nstxtcout= 1 xtc_precision= 1000 xtc_grps = energygrps = nstlist = 10 ns_type = grid pbc = xyz rlist= 0.9 domain-decomposition = no coulombtype = PME fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-05 optimize_fft = no epsilon_surface = 0 ewald_geometry = 3d rcoulomb = 0.9 vdwtype = Cut-off rvdw = 0.9 epsilon_r= 1 DispCorr = EnerPres ; with sd as integrator tcoupl is ignored tc-grps = system ; good choice for zeta is 0.5 1/s tau_t= 2.0 ref_t= 310 pcoupl = berendsen pcoupltype = anisotropic nstpcouple = -1 tau_p= 1.0 compressibility = 4.6e-5 4.6e-5 4.6e-5 0 0 0 ref_p= 1.0 1.0 1.0 0.0 0.0 0.0 annealing= no ;annealing_npoints = 3 ;annealing_time = 0 gen_vel = no gen_temp = 310 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS continuation = no lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 morse= no disre= no disre_weighting = equal disre_mixed = no disre_fc = 1000 disre_tau= 10 nstdisreout = 1000 Parameters that are different in my advisor's file: DispCorr = Ener tau_t= 0.20 compressibility = 5e-6 5e-6 5e-6 0 0 0 gen_vel = yes gen_temp = 1 gen_seed = 473529 I thought when using vdw cutoff, it is recommended to use dispersion corrections for both pressure and energy. Also can some explain the reason behind this? For tau_t, I used 2 as it is the recommended value for sd integrator in the manual. Also gen_vel has to be no for sd integrator, correct? Any help will be appreciated! Thanks in advance, Shyno -- Shyno Mathew PhD student Department of Chemical Engineering Columbia University -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Tabulated potential segmentation fault
On Fri, 2012-04-13 at 11:01 +1000, Mark Abraham wrote: On 13/04/2012 2:48 AM, Laura Leay wrote: All, I'm trying to run a tabulated soft core potential with the form V = A + Br^2 + Cr^3 up to about r=0.1 A and the normal LJ 6-12 potential after this. I've chosen the parameters of this equation to be the same for all atoms in my system (a polymer containing carbon, nitrogen and hydrogen). I've not assigned any charges to the system. Running on Gromacs version 4.5.4 single precision on a high perfomance computing cluster the first 50 or so steps run fine, energies seem reasonable but then the simulation crashes with a segmentation fault. I submitted the job using the comand mdrun -table table.xvg -v -nt $NSLOTS -pd The job seems to run ok on my own desktop PC although I've not tried running it for more than a few minutes to check that it would indeed run. If anyone can tell me why this won't run on the computing cluster I'd appreciate it. the first few lines of my table file look like this: 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.150E+05 0.000E+00 0.200E-02 0.000E+00 0.000E+00 0.3045913E-01 -0.4568869E+02 0.1499547E+05 0.4525801E+04 0.400E-02 0.000E+00 0.000E+00 0.2436730E+00 -0.1827548E+03 0.1498190E+05 0.9051602E+04 0.600E-02 0.000E+00 0.000E+00 0.8223965E+00 -0.4111982E+03 0.1495927E+05 0.1357740E+05 0.800E-02 0.000E+00 0.000E+00 0.1949384E+01 -0.7310191E+03 0.1492759E+05 0.1810320E+05 0.100E-01 0.000E+00 0.000E+00 0.3807391E+01 -0.1142217E+04 0.1488685E+05 0.2262901E+05 0.120E-01 0.000E+00 0.000E+00 0.6579172E+01 -0.1644793E+04 0.1483707E+05 0.2715481E+05 0.140E-01 0.000E+00 0.000E+00 0.1044748E+02 -0.2238746E+04 0.1477824E+05 0.3168061E+05 0.160E-01 0.000E+00 0.000E+00 0.1559507E+02 -0.2924076E+04 0.1471035E+05 0.3620641E+05 0.180E-01 0.000E+00 0.000E+00 0.2220471E+02 -0.3700784E+04 0.1463341E+05 0.4073221E+05 0.200E-01 0.000E+00 0.000E+00 0.3045913E+02 -0.4568869E+04 0.1454742E+05 0.4525801E+05 0.220E-01 0.000E+00 0.000E+00 0.4054110E+02 -0.5528332E+04 0.1445238E+05 0.4978381E+05 This is my mdp file (note that I turned dispersion correction off to see if this was the problem but it would seem that it is not): ; VARIOUS PREPROCESSING OPTIONS title= Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ;md for simulation, steep for Emin ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps =10; 100 ;for simulation ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed ;bd-temp = 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 50 nstenergy= 50 ; Output frequency and precision for xtc file nstxtcout= 50 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ;
Re: [gmx-users] GROMOS87 and CHARMM27
On 2012-04-16 08:26:00AM -0700, Shima Arasteh wrote: Dear GROMACS users, I reproduced the results of a protein-membrane system by using force field GROMOSE87. This protein forms ion channel in membrane. Now if I wanna study the ion conduction through this channel using force field CHARMM27 in umbrella sampling method, is it possible? Can I use the results of the system simulation which has been derived by GROMOS87? By definition, switching to a different forcefield like that usually requires the regeneration of the system's topology, so your new system will be different from your old one anyway. In addition, you may need to rename the atoms in the coordinate files obtained from previous gromos runs to match those in the charmm27 residue files. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Tabulated potential segmentation fault
On 17/04/2012 1:50 AM, Laura Leay wrote: On Fri, 2012-04-13 at 11:01 +1000, Mark Abraham wrote: On 13/04/2012 2:48 AM, Laura Leay wrote: All, I'm trying to run a tabulated soft core potential with the form V = A + Br^2 + Cr^3 up to about r=0.1 A and the normal LJ 6-12 potential after this. I've chosen the parameters of this equation to be the same for all atoms in my system (a polymer containing carbon, nitrogen and hydrogen). I've not assigned any charges to the system. Running on Gromacs version 4.5.4 single precision on a high perfomance computing cluster the first 50 or so steps run fine, energies seem reasonable but then the simulation crashes with a segmentation fault. I submitted the job using the comand mdrun -table table.xvg -v -nt $NSLOTS -pd The job seems to run ok on my own desktop PC although I've not tried running it for more than a few minutes to check that it would indeed run. If anyone can tell me why this won't run on the computing cluster I'd appreciate it. the first few lines of my table file look like this: 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.150E+05 0.000E+00 0.200E-02 0.000E+00 0.000E+00 0.3045913E-01 -0.4568869E+02 0.1499547E+05 0.4525801E+04 0.400E-02 0.000E+00 0.000E+00 0.2436730E+00 -0.1827548E+03 0.1498190E+05 0.9051602E+04 0.600E-02 0.000E+00 0.000E+00 0.8223965E+00 -0.4111982E+03 0.1495927E+05 0.1357740E+05 0.800E-02 0.000E+00 0.000E+00 0.1949384E+01 -0.7310191E+03 0.1492759E+05 0.1810320E+05 0.100E-01 0.000E+00 0.000E+00 0.3807391E+01 -0.1142217E+04 0.1488685E+05 0.2262901E+05 0.120E-01 0.000E+00 0.000E+00 0.6579172E+01 -0.1644793E+04 0.1483707E+05 0.2715481E+05 0.140E-01 0.000E+00 0.000E+00 0.1044748E+02 -0.2238746E+04 0.1477824E+05 0.3168061E+05 0.160E-01 0.000E+00 0.000E+00 0.1559507E+02 -0.2924076E+04 0.1471035E+05 0.3620641E+05 0.180E-01 0.000E+00 0.000E+00 0.2220471E+02 -0.3700784E+04 0.1463341E+05 0.4073221E+05 0.200E-01 0.000E+00 0.000E+00 0.3045913E+02 -0.4568869E+04 0.1454742E+05 0.4525801E+05 0.220E-01 0.000E+00 0.000E+00 0.4054110E+02 -0.5528332E+04 0.1445238E+05 0.4978381E+05 This is my mdp file (note that I turned dispersion correction off to see if this was the problem but it would seem that it is not): ; VARIOUS PREPROCESSING OPTIONS title= Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ;md for simulation, steep for Emin ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps =10; 100 ;for simulation ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed ;bd-temp = 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 50 nstenergy= 50 ; Output frequency and precision for xtc file nstxtcout= 50 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = simple ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 0.9 domain-decomposition = no ; OPTIONS FOR
Re: [gmx-users] Protein ligand molecular dynamics simulation
On Mon, Apr 16, 2012 at 11:01 PM, sai nitin sainit...@gmail.com wrote: Hi all, I have done complex (protein + ligand) complex from autodock software using this complex im trying to follow http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html tutorial But when i take complex structure directly from autodock result and run PDB2GMX it will give error because it is not recognizing ligand topology which is in complex structure. Then i followed justin tutorial took protein alone and applied Charmm27 Force field and used generate ligand topologies using Swissparam tool (http://swissparam.ch/) when i do Editconf and created cubic box ligand is going away from protein. Actually my main task to place ligand in paraticular binding site in my protein and perform molecular dynamics. Can any body tell me how to do this..? 1] pdb2gmx generate ligands.top (if possible, basically you need generate your ligand.itp by other ways) and rename it as ligands.itp 2] pdb2gmx generate protein.top and rename it as protein.itp (also need delete some entry) 3] create the topol.top includes the ligands.itp and protein.itp, take care the double entry. (To make it easy, you may take some pdb with several chains. use pdb2gmx and see how those top files combined together.) 4] The docked structure skip the pdb2gmx step. go directly to the editconf. You may do a try, but it will be helpful if you are a bit familiar with how to combine those top_files. Thanks in advance -- Sainitin D -- 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: Re: NPT simulation for mutation study
Hello Prof. David, thanks for your reply. I will try using isotropic pressure scaling. But still I am not clear why the simulations ran fine with first .mdp file. As mentioned in the previous email only few parameters were different in my .mdp file compared to my advisor's. I am just copying those parameters again: Parameters that are different in my advisor's file: DispCorr = Ener tau_t= 0.20 compressibility = 5e-6 5e-6 5e-6 0 0 0 gen_vel = yes gen_temp = 1 gen_seed = 473529 can including dispersion corrections for pressure induce such a huge change? thanks Shyno -- Shyno Mathew PhD student Department of Chemical Engineering Columbia University -- 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: Re: NPT simulation for mutation study
Shyno Mathew wrote: Hello Prof. David, thanks for your reply. I will try using isotropic pressure scaling. But still I am not clear why the simulations ran fine with first .mdp file. As mentioned in the previous email only few parameters were different in my .mdp file compared to my advisor's. I am just copying those parameters again: Parameters that are different in my advisor's file: DispCorr = Ener tau_t= 0.20 compressibility = 5e-6 5e-6 5e-6 0 0 0 gen_vel = yes gen_temp = 1 gen_seed = 473529 can including dispersion corrections for pressure induce such a huge change? By changing several variables at once, it becomes hard (read: almost impossible) to say what caused it. By also not generating velocities (assuming this is step 1 in equilibration), you can induce instability. The real lesson is you shouldn't make haphazard changes or take anything for granted as far as settings that should work. Spending a few hours reading the literature will save you weeks of troubleshooting an elusive problem. -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] GROMOS87 and CHARMM27
So, I can not use the coordinates of the output files of gromos runs. Right? From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, April 16, 2012 8:23 PM Subject: Re: [gmx-users] GROMOS87 and CHARMM27 On 2012-04-16 08:26:00AM -0700, Shima Arasteh wrote: Dear GROMACS users, I reproduced the results of a protein-membrane system by using force field GROMOSE87. This protein forms ion channel in membrane. Now if I wanna study the ion conduction through this channel using force field CHARMM27 in umbrella sampling method, is it possible? Can I use the results of the system simulation which has been derived by GROMOS87? By definition, switching to a different forcefield like that usually requires the regeneration of the system's topology, so your new system will be different from your old one anyway. In addition, you may need to rename the atoms in the coordinate files obtained from previous gromos runs to match those in the charmm27 residue files. -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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 simulation for mutation study (Justin A. Lemkul)
Hey Justin, thanks for your reply. For gen_vel, the manual says Generate velocities in grompp according to a Maxwell distribution at temperature gen_temp [K], with random seed gen_seed. This is only meaningful with integrator md Since the integrator I am using is sd, I put 'gen_vel no' Yes you are correct, this is equilibration. From what you are saying, even with sd as the integrator, I guess, I should put gen_vel yes gen_temp 310 ; i want to do the simulation at 310K thanks -- Shyno Mathew PhD student Department of Chemical Engineering Columbia University -- 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] GROMOS87 and CHARMM27
On 2012-04-16 10:14:01AM -0700, Shima Arasteh wrote: So, I can not use the coordinates of the output files of gromos runs. Right? You can but you may need to rename the atoms for each residue for pdb2gmx to work. From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, April 16, 2012 8:23 PM Subject: Re: [gmx-users] GROMOS87 and CHARMM27 On 2012-04-16 08:26:00AM -0700, Shima Arasteh wrote: Dear GROMACS users, I reproduced the results of a protein-membrane system by using force field GROMOSE87. This protein forms ion channel in membrane. Now if I wanna study the ion conduction through this channel using force field CHARMM27 in umbrella sampling method, is it possible? Can I use the results of the system simulation which has been derived by GROMOS87? By definition, switching to a different forcefield like that usually requires the regeneration of the system's topology, so your new system will be different from your old one anyway. In addition, you may need to rename the atoms in the coordinate files obtained from previous gromos runs to match those in the charmm27 residue files. -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] GROMOS87 and CHARMM27
Shima Arasteh wrote: So, I can not use the coordinates of the output files of gromos runs. Right? Not without significant modification of names, presence of H atoms, etc. You'll need to regenerate a suitable topology, as has been said, and then run thorough equilibration under the new force field. -Justin *From:* Peter C. Lai p...@uab.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Monday, April 16, 2012 8:23 PM *Subject:* Re: [gmx-users] GROMOS87 and CHARMM27 On 2012-04-16 08:26:00AM -0700, Shima Arasteh wrote: Dear GROMACS users, I reproduced the results of a protein-membrane system by using force field GROMOSE87. This protein forms ion channel in membrane. Now if I wanna study the ion conduction through this channel using force field CHARMM27 in umbrella sampling method, is it possible? Can I use the results of the system simulation which has been derived by GROMOS87? By definition, switching to a different forcefield like that usually requires the regeneration of the system's topology, so your new system will be different from your old one anyway. In addition, you may need to rename the atoms in the coordinate files obtained from previous gromos runs to match those in the charmm27 residue files. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst| KAUL 752A Genetics, Div. of Research| 705 South 20th Street p...@uab.edu mailto:p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808| == -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: NPT simulation for mutation study (Justin A. Lemkul)
Shyno Mathew wrote: Hey Justin, thanks for your reply. For gen_vel, the manual says Generate velocities in grompp according to a Maxwell distribution at temperature gen_temp [K], with random seed gen_seed. This is only meaningful with integrator md Since the integrator I am using is sd, I put 'gen_vel no' Ah, I guess I missed that before. Yes you are correct, this is equilibration. From what you are saying, even with sd as the integrator, I guess, I should put gen_vel yes gen_temp 310 ; i want to do the simulation at 310K As I said before, you've changed too many variables simultaneously (not very scientific ;) to pinpoint exactly what the problem is. Systematic changes, as prescribed by your force field and chosen algorithms, are the only suitable way to run a simulation. Right now, it's a pure guess as to what went wrong. -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
[gmx-users] ewald_rtol
Hi, Does the parameter ewald_rtol affect PME electrostatics (coulombtype = PME), or does ewald_rtol only affect Ewald electrostatics (coulombtype = Ewald)? In the manual description of the .mdp parameters (http://manual.gromacs.org/current/online/mdp_opt.html#el), it says in the Ewald section, The relative accuracy of direct/reciprocal space is controlled by ewald_rtol. Similarly, page 100 of the manual says, The ewald_rtol parameter is the relative strength of the electrostatic interaction at the cut-off. Decreasing this gives you a more accurate direct sum, but a less accurate reciprocal sum. However, I do not see ewald_rtol specifically discussed in any of the manual sections on PME. Does this mean that ewald_rtol is only relevant for the (normal, classical) Ewald sum electrostatics? Thank you! Andrew DeYoung Carnegie Mellon University -- 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] ewald_rtol
Andrew DeYoung wrote: Hi, Does the parameter ewald_rtol affect PME electrostatics (coulombtype = PME), or does ewald_rtol only affect Ewald electrostatics (coulombtype = Ewald)? In the manual description of the .mdp parameters (http://manual.gromacs.org/current/online/mdp_opt.html#el), it says in the Ewald section, The relative accuracy of direct/reciprocal space is controlled by ewald_rtol. Similarly, page 100 of the manual says, The ewald_rtol parameter is the relative strength of the electrostatic interaction at the cut-off. Decreasing this gives you a more accurate direct sum, but a less accurate reciprocal sum. However, I do not see ewald_rtol specifically discussed in any of the manual sections on PME. Does this mean that ewald_rtol is only relevant for the (normal, classical) Ewald sum electrostatics? It is related to PME. http://lists.gromacs.org/pipermail/gmx-users/2009-February/039806.html There are a number of other discussions about it in the list archive; I'd suggest you have a look. -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
[gmx-users] What is epsilon_r?
Hi, What is the parameter epsilon_r mentioned in the manual (http://manual.gromacs.org/current/online/mdp_opt.html#el)? The manual says that it is the relative dielectric constant. My initial thought was that this would only be relevant for reaction-field electrostatics, or somewhere where implicit solvent is used. However, it seems that epsilon_rf (not epsilon_r) is used for reaction-field purpose. I am not using implicit solvent in my system, nor am I using a reaction-field method (I am using PME electrostatics); in my system, I am using an all-atom description. Then, does epsilon_r generate additional dielectric, beyond what naturally arises from the all-atom description of the solvent? Even though I am not using a reaction-field method, epsilon_r is clearly affecting something, because when I use g_potential to calculate the electric potential, the results vary considerably depending on the value of epsilon_r that I use in my .mdp file. Do you have any thoughts about what epsilon_r does in an all-atom descripton of a solvent? Does it provide additional charge screening? Thank you kindly! Andrew DeYoung Carnegie Mellon University -- 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] What is epsilon_r?
Andrew DeYoung wrote: Hi, What is the parameter epsilon_r mentioned in the manual (http://manual.gromacs.org/current/online/mdp_opt.html#el)? The manual says that it is the relative dielectric constant. My initial thought was that this would only be relevant for reaction-field electrostatics, or somewhere where implicit solvent is used. However, it seems that epsilon_rf (not epsilon_r) is used for reaction-field purpose. I am not using implicit solvent in my system, nor am I using a reaction-field method (I am using PME electrostatics); in my system, I am using an all-atom description. Then, does epsilon_r generate additional dielectric, beyond what naturally arises from the all-atom description of the solvent? Even though I am not using a reaction-field method, epsilon_r is clearly affecting something, because when I use g_potential to calculate the electric potential, the results vary considerably depending on the value of epsilon_r that I use in my .mdp file. Do you have any thoughts about what epsilon_r does in an all-atom descripton of a solvent? Does it provide additional charge screening? http://lists.gromacs.org/pipermail/gmx-users/2004-March/009650.html -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
[gmx-users] Re: temperature
Mark, According to the manual, the temperature of a group should always be calculated from the total KE of the group (see eq 3.13 in the manual), which presumably includes contributions from the translational motion of the center of mass of the group, plus the rotational motion around the center of mass of the group, plus any random non-rigid motion within the group. However, according to appendix D.72 for g_traj, the option –ot plots the temperature of each group calculated only from the rigid body translational velocity of the center of mass of the group, since the command –ot implies –com. Aren’t these two definitions of temperature incompatible, since the –ot definition ignores two terms (rotational and random)? Roy -- View this message in context: http://gromacs.5086.n6.nabble.com/temperature-tp4658469p4888099.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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] Is GPU GTX 560 compatible with GROMACS?
Dear Shouliang, Thanks. Maybe the developers can help undertand why GTX560 is not included on the GPU compatibility list for GROMACS? -G 2012/4/16 shouliang dong shouliangd...@gmail.com: It is compatible with GROMACS. 在 2012年4月14日 上午11:32，Gaurav Goel gauravgoel...@gmail.com写道： Dear All, Can you please guide me on how to find out if GeForce GTX 560 GPU card by NVIDIA will be compatible with GROMACS? On the website GTX 560 Ti is mentioned, but GTX 560 is not. Thanks, G -- Gaurav Goel, PhD Assistant Professor Department of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016 India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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 -- Gaurav Goel, PhD Assistant Professor Department of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016 India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
