[gmx-users] Re: Isovalue for g_spatial representation
Dear Chris, thank you for information, they were very enlightening. Just one more question. Suppose I use an isovalue, say 10, I can say that the drawn surface is 10 times the average number density of solvent molecules? I am using -div option. Bests eef ___ Eudes Eterno Fileti Física da Matéria Condensada Simulação Computacional de Nano-estruturas via Dinâmica Molecular Message: 2 Date: Fri, 29 Oct 2010 19:53:38 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] Isovalue for g_spatial representation To: gmx-users@gromacs.org Message-ID: 20101029195338.kzvrdcvjr440c...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed eef, I wrote g_spatial. If you use the -nodiv option, then the iso-value represents the number of counts in that bin over the entire trajectory divided by the number of frames. Therefore the units would be atomic occupancy counts per frame. Note that, as for all such histograms, the values of isolines and isosurfaces are dependent on bin size. If you use the -div option (default), then the counts (already divided by the number of frames) are further divided by the number of atoms in the selection and then multiplied by the number of cells (similar to dividing by the volume of each cell). It's really a lot like an RDF: a number density per grid divided by the overall system density. It is, however, related to this by some multiplicative constant. You can find that because at the end of a g_density -div run, you will get an output of exactly what this divisor was, so you can go in using awk or whatever you like and modify the values as you see fit, turning values into proper densities if you like. Alternatively, you can run -nodiv and then divide all the the values yourself to get a proper density. Chris. -- original message -- Hello gmx-users. I calculated the spatial distribution functions for my solvent-solute system. However I am in doubt in relation to the isovalue to be used in VMD to control the representation of the surface. The isovalue is admensional number or has some unit? There is some special criterium to choose its value? Thank you in advance. eef -- -- 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! End of gmx-users Digest, Vol 78, Issue 225 ** -- 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] trjconv -pbc
Hi gmx users Perhaps, this question be repetitive. I want to know using trjconv -pbc is only a solution for visualization problem? Is there feasibility to use old trajectory file (with out trjconv -pbc) for any kind of analysis without any problem? -- Atila Petrosian Ph.D. student of BioPhysical Chemistry University of Oulu,Finland -- 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] trjconv -pbc
atila petrosian wrote: Hi gmx users Perhaps, this question be repetitive. I want to know using trjconv -pbc is only a solution for visualization problem? Is there feasibility to use old trajectory file (with out trjconv -pbc) for any kind of analysis without any problem? Most Gromacs tools handle PBC internally, so using trjconv is not required. There are some tools, however (g_rms, g_gyrate, etc) that do not, thus requiring a fixed trajectory. There was some discussion about this topic just the other day; please check the list archive. -Justin -- Atila Petrosian Ph.D. student of BioPhysical Chemistry University of Oulu,Finland -- 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] yes/no
Hi gromacs users In gromacs manual, in appendix section, for every tool, in Files section, there are input and output files needed for analysis. but in Other options section, there are some things that I don't understand. Is third column of Other opthions default values? In third column of Other opthions, somewhen, yes or no is seen. What does yes mean? What does no mean? any help will highly appreciated. -- 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] yes/no
shahab shariati wrote: Hi gromacs users In gromacs manual, in appendix section, for every tool, in Files section, there are input and output files needed for analysis. but in Other options section, there are some things that I don't understand. Is third column of Other opthions default values? Yes. In third column of Other opthions, somewhen, yes or no is seen. What does yes mean? What does no mean? Yes means the option is applied, no means it is not. It is a simple boolean condition. For instance, with editconf, using editconf -c means the solute is centered, editconf -noc means it is not. -Justin any help will highly appreciated. -- 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] yes/no
Hi Justin thanks for your attention. in editconf instance, if I don't use -c, this is same mean with -noc? In third column of Other opthions, somewhen, 1 and -1 is seen. What does 1 mean? What does -1 mean? -- 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] yes/no
Dear Justin I understood. for instance, in trjconv -dump (-1), What does it mean? -- 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] yes/no
shahab shariati wrote: Dear Justin I understood. for instance, in trjconv -dump (-1), What does it mean? It means that a frame is not dumped. Time values must be positive, so -1 does not correspond to any time in the trajectory. -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] yes/no
Dear Justin thanks thus, if I want to set 800 ps for -dump, -dump 796 is true (every frame is 4 ps). ok? -- 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] yes/no
shahab shariati wrote: Dear Justin thanks thus, if I want to set 800 ps for -dump, -dump 796 is true (every frame is 4 ps). ok? You can answer this yourself by doing it. -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] LINCS vs SHAKE
Sai Pooja wrote: For Replica exchange, is there any advantage of in using SHAKE over LINCS(other than the stepsize)? I am running an REM simulation and the simulation stops after running for variable number of steps (10, 1000 etc.) because some bond moves more than 30 degrees and LINCS gives a warning. It has been said (check the archive) that LINCS is more stable. Just because you're getting LINCS warnings does not mean the constraint algorithm is to blame, it's just the first algorithm that fails when your model physics implodes. -Justin Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- 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] New release: 4.5.2
Dear Gromacs users and developers, A new bugfix release of Gromacs is now available: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.2.tar.gz. Here is a list of some of the resolved issues for 4.5.1: * CHARMM force field now has single atom charge groups (pdb2gmx -nochargegrp no longer required) * Made pdb2gmx -chainsep option work * Fixed possible inconvenient npme node choice with pme load between 0.33 and 0.50 which could lead to very slow mdrun performance. * Made Generalized Born gb_algorithm and sa_surface_tension active and added a separate non-polar solvation term to the output. * Fixed issues in Generalized Born code that could cause incorrect results with SSE and all-vs-all inner-loops. * Fixed bug with pressure coupling with nstlist=-1 that resulted in extremely low densities. * Fixed corrupted energy and checkpoint file output with BAR free energy calculations. * Fixed normalization of g_density using only the last frame. * Fixed several issues with cmake * Several minor fixes. Once again big thanks to all developers for their hard work, and to all users for their contributions! Happy simulating! Rossen -- 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] New release: 4.5.2
Hi, I have a few questions/comments about the application of the single atom charge groups with the CHARMM27 force field that maybe someone can help with: 1. There are some entries in aminoacids.rtp which have not been converted to having every atom in a separate charge group (ASPP, CYS2, GLUP, LSN, HEME, HEO2, O2, C2 and HOH, hopefully I didn't miss any!). I understand these are some of the less commonly used entries, have they been left out for a reason? By the way I also noticed during a quick test for this that there is not an rtp entry for ARGN but it is given as an option by pdb2gmx when using -inter. 2. Relating to 1 are the charge groups in the water models, which have also been left as a water in a single charge group. I think I remember reading somewhere that this is needed for the fast water loops in GROMACS, so I assume this has been done on purpose. My concern is that this is different to the TIP3P and TP3M entries in the aminoacids.rtp file. If this has been done on purpose for the water models, then maybe TIP3 and TP3M should also just have one charge group (as in the HOH entry)? 3. Finally, another concern I have is that when adding termini to a protein (from aminoacids.c.tdb and aminoacids.n.tdb) then the terminal atoms are still added as one charge group by pdb2gmx. I am not sure of a way around this, apart from still using the -nochargegrp option, or having AMBER style rtp entries for the N and C terminal residues (undesirable I am sure). Cheers Tom On 30/10/10 20:56, Rossen Apostolov wrote: Dear Gromacs users and developers, A new bugfix release of Gromacs is now available: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.2.tar.gz. Here is a list of some of the resolved issues for 4.5.1: * CHARMM force field now has single atom charge groups (pdb2gmx -nochargegrp no longer required) * Made pdb2gmx -chainsep option work * Fixed possible inconvenient npme node choice with pme load between 0.33 and 0.50 which could lead to very slow mdrun performance. * Made Generalized Born gb_algorithm and sa_surface_tension active and added a separate non-polar solvation term to the output. * Fixed issues in Generalized Born code that could cause incorrect results with SSE and all-vs-all inner-loops. * Fixed bug with pressure coupling with nstlist=-1 that resulted in extremely low densities. * Fixed corrupted energy and checkpoint file output with BAR free energy calculations. * Fixed normalization of g_density using only the last frame. * Fixed several issues with cmake * Several minor fixes. Once again big thanks to all developers for their hard work, and to all users for their contributions! Happy simulating! Rossen -- Dr Thomas Piggot University of Southampton, UK. -- 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] LINCS vs SHAKE
Justin is probably correct, your system is unstable. However, let me mention another possibility. As the temperature increases, the largest stable timestep decreases in length. Is it possible that over some temperature (1000K?) a 2 fs timestep is no longer viable? In this case, even a well minimized system with a large number for lincs_iter is still going to give you incorrect sampling and possibly crash. You'd need to reduce you highest temperature or reduce your timestep. I don't know if the gromacs REMD algorithm allows you to use a smaller timestep at higher temperatures, but it's something to look into. Chris. -- original message -- For Replica exchange, is there any advantage of in using SHAKE over LINCS(other than the stepsize)? I am running an REM simulation and the simulation stops after running for variable number of steps (10, 1000 etc.) because some bond moves more than 30 degrees and LINCS gives a warning. Pooja -- 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] Isovalue for g_spatial representation
No you can not do that. You can only say that it is drawn at N times the average number density of solvent molecules. To determine N, find out the average grid.cube value in a region of pure solvent, let that value be A, and N=10/A. Clearly you're trying to do a figure caption, and I'm sorry that the tool does not do this for you. There are technical issues that make it harder than you might think to automate although it certainly could be done. You can estimate A by sliding the bar in VMD and A is next to where the bulk water disappears. This will give you an estimate that you can later use to ensure that your quantitative value is correct. To get the quantitative value, you'll probably need to run awk over the grid.cube file and average over a predefined section. Careful though, don't go all the way to the boundaries of the cube, the corners there are likely low density due to rotation from trjconv. Chris. -- original message -- Dear Chris, thank you for information, they were very enlightening. Just one more question. Suppose I use an isovalue, say 10, I can say that the drawn surface is 10 times the average number density of solvent molecules? I am using -div option. Bests eef -- 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] LINCS vs SHAKE
On 31/10/2010 10:04 AM, chris.ne...@utoronto.ca wrote: Justin is probably correct, your system is unstable. However, let me mention another possibility. As the temperature increases, the largest stable timestep decreases in length. Is it possible that over some temperature (1000K?) a 2 fs timestep is no longer viable? In this case, even a well minimized system with a large number for lincs_iter is still going to give you incorrect sampling and possibly crash. You'd need to reduce you highest temperature or reduce your timestep. I don't know if the gromacs REMD algorithm allows you to use a smaller timestep at higher temperatures, but it's something to look into. It doesn't. Off the cuff, I can't say whether it's sound to simulate at a smaller timestep at higher temperature and exchange with a simulation that has done the same number of larger timesteps. Mark Chris. -- original message -- For Replica exchange, is there any advantage of in using SHAKE over LINCS(other than the stepsize)? I am running an REM simulation and the simulation stops after running for variable number of steps (10, 1000 etc.) because some bond moves more than 30 degrees and LINCS gives a warning. Pooja -- 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] LINCS vs SHAKE
I would look for an error in the input files first. However, I have a suspicion that this artifact is most likely from a thermostat problem than LINCS. LINCS may be the object that is throwing the exception, but in a recent paper by Rosta et.al., it was shown that weak-coupling thermostats (such as the Berendsen thermostat) that produce noncanonical ensembles (narrowed fluctuation amplitude) undergo significant configuration-space distortion under REMD simulations. This causes an artificial bias towards exchange of replicas at the high and low end of the temperature scale. In other words, at some point during REMD, LINCS ends up having to deal with a superheated replica showing up at the colder energy levels, forcing it to cope with extremely high differences in velocity. Switching to a stronger coupling thermostat may be required in these cases. J. Chem. Theory Comput., 2009, 5 (5), pp 1393?1399 ~jared Quoting chris.ne...@utoronto.ca: Justin is probably correct, your system is unstable. However, let me mention another possibility. As the temperature increases, the largest stable timestep decreases in length. Is it possible that over some temperature (1000K?) a 2 fs timestep is no longer viable? In this case, even a well minimized system with a large number for lincs_iter is still going to give you incorrect sampling and possibly crash. You'd need to reduce you highest temperature or reduce your timestep. I don't know if the gromacs REMD algorithm allows you to use a smaller timestep at higher temperatures, but it's something to look into. Chris. -- original message -- For Replica exchange, is there any advantage of in using SHAKE over LINCS(other than the stepsize)? I am running an REM simulation and the simulation stops after running for variable number of steps (10, 1000 etc.) because some bond moves more than 30 degrees and LINCS gives a warning. Pooja -- 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 thewww 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] LINCS vs SHAKE
Mark, I am quite sure that a difference in the overall simulation time between two replicas is not going to introduce any bias. Still, you bring up a good point. If the energy distribution (or even worse, its average) at a given temperature is affected by the timestep, then this would be a bad idea. Given the difficulties in converging ST A-values or (even harder) SREM PDFs, I'm not sure if the answer to this is known, but I would bet that the timestep is going to influence this now that you point it out. Chris. -- original message -- On 31/10/2010 10:04 AM, chris.neale at utoronto.ca wrote: Justin is probably correct, your system is unstable. However, let me mention another possibility. As the temperature increases, the largest stable timestep decreases in length. Is it possible that over some temperature (1000K?) a 2 fs timestep is no longer viable? In this case, even a well minimized system with a large number for lincs_iter is still going to give you incorrect sampling and possibly crash. You'd need to reduce you highest temperature or reduce your timestep. I don't know if the gromacs REMD algorithm allows you to use a smaller timestep at higher temperatures, but it's something to look into. It doesn't. Off the cuff, I can't say whether it's sound to simulate at a smaller timestep at higher temperature and exchange with a simulation that has done the same number of larger timesteps. Mark Chris. -- original message -- For Replica exchange, is there any advantage of in using SHAKE over LINCS(other than the stepsize)? I am running an REM simulation and the simulation stops after running for variable number of steps (10, 1000 etc.) because some bond moves more than 30 degrees and LINCS gives a warning. -- 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
