Re: [gmx-users] Test particle insertion for all atom force field
Hi, You can put the entire molecule the the end of .gro file, it shall work. Remember that the molecule should be centered at 0, 0, 0. João On Thu, Apr 6, 2017 at 1:06 PM, Badmos, Sakiru wrote: > Hi everyone, > > I want to calculate excess chemical potential for some > molecules in water. I found a tutorial on this but it was on methane > (united atom). The insertion of the test particle requires that it is > included as the last atom in the .gro file with coordinate 0.000 0.000 > 0.000. This works for United atom. How do I do this for molecule like CO2 > with three atoms? > > Thank you as you help. > > Sakiru. > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Parameterization for noval molecules.
Dear Gromacs users. Can anybody who are good in parameterization, make parameters for the molecule of my interest..As i am a beginner and was told on this forum that parameterization is not for beginners. Thanks.. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to write pull code in umbrella sampling
Thank you so much, Justin. I will look into PLUMED. Qing At 2017-04-08 19:05:28, "Justin Lemkul" wrote: > > >On 4/8/17 1:46 AM, Qing Lv wrote: >> Thank you, Justin. >> >> >> My goal is to investigate the conformation transition of a 30aa loop between >> an unstructured loop and an alpha-helix. I found a transition pathway on >> free energy landscape and selected a number of frames along the pathway for >> umbrella sampling. So, should I define C-alpha of this 30aa loop as >> pull-group1 and C-alpha of the remaining part as pull-group2 ? Would the >> pull geometry still be "distance"? But this will just restrain the distance >> between COM of the 2 groups to the initial distance, but cannot restrain the >> conformation of the loop. >> Or need I divide the loop into many small segments (pull-groups) and define >> the pull coordinates separately? This seems horrible... >> > >You should probably be looking at a more advanced, multi-dimensional bias or >collective variable. Look into PLUMED. GROMACS is going to be limited to a >linear reaction coordinate, which may not capture everything you need in such >a >large transition. > >-Justin > >> >> Thanks, >> Qing >> >> >> At 2017-04-08 09:06:46, "Justin Lemkul" wrote: >>> >>> >>> On 4/7/17 8:56 PM, Qing Lv wrote: Dear Colleagues, I am trying to do an umbrella sampling using a series of conformations extracted from several unbiased MD trajectories. But I am not sure about the pull code in .mdp file. Below is the pull code from the tutorial of Dr. Justin Lemkul : define = -DPOSRES_B ; (Why ??) >>> >>> Did you read the paper I linked from the tutorial, which explains why this >>> is >>> done for this very specific case? >>> ; Pull code pull= yes pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= Chain_B pull_group2_name= Chain_A pull_coord1_type= umbrella ; harmonic biasing force pull_coord1_geometry= distance ; simple distance increase pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_coord1_rate= 0.0 pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 Conformations in Justin's tutorial are from steered MD. However, my conformations are not from SMD, and I have not done SMD on this system. So, how to define pull_group1 and pull_group2? And pull_coord1_geometry still set to "distance" ? >>> >>> The pull groups don't depend on where the configurations came from. They >>> define >>> the reaction coordinate. You can use whatever pull geometry makes sense; >>> in the >>> tutorial it is a simple linear reaction coordinate directly along the >>> z-axis. >>> Other applications may require different definitions. >>> Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES ") ? Why? >>> >>> Generally, no, but you haven't given any useful detail about what your >>> simulation system is. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> == >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send >>> a mail to gmx-users-requ...@gromacs.org. > >-- >== > >Justin A. Lemkul, Ph.D. >Ruth L. Kirschstein NRSA Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 629 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 >http://mackerell.umaryland.edu/~jalemkul > >== >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/
Re: [gmx-users] TOPOLBUILD
On Apr 8, 2017, at 13:34:08 +0530 Vidya Devi wrote: wrote: > Hi gromacs users, > > I am using topolbuild to generate oplsaa force field parameters. > > ./topolbuild -n LIGAND.mol2 -dir > C:/cygwin64/usr/local/gromacs/share/gromacs/top/oplsaa.ff -meas > Need correct parameters > >. > > What should I do to get correct parameters? > > Thanks, > Vidya.R The correct parameters are included with the topolbuild files. In the topolbuild package, there is a directory called dat Whereever you placed that directory is where the -dir parameter should be pointed. Ordinarily, one would run topolbuild in the directory of the mol2 file from which the topology is to be built. This ensures that the topology is built in the same directory as the mol2 file and _not_ in the directory of the topolbuild binary. Thus, for oplsaa, one would write a command that has a general form: /path_to_topolbuild/topolbuild -n LIGAND -dir /path_to_topolbuild_data/dat/gromacs -ff oplsaa Note that the directory pointed to is a topolbuild directory and not part of the gromacs distribution, and not to a specific forcefield file. This is because automatic topology generation needs more atom typing information. Examples of commands are given in the file PROGRAM_TESTING DONE.txt General explanation of program commands is given in the file README.txt Warnings about the limitations of automatic topology generation are given in the file limitations.txt -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St., Rm. LD-061 Indianapolis, IN 46202 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to write pull code in umbrella sampling
On 4/8/17 1:46 AM, Qing Lv wrote: Thank you, Justin. My goal is to investigate the conformation transition of a 30aa loop between an unstructured loop and an alpha-helix. I found a transition pathway on free energy landscape and selected a number of frames along the pathway for umbrella sampling. So, should I define C-alpha of this 30aa loop as pull-group1 and C-alpha of the remaining part as pull-group2 ? Would the pull geometry still be "distance"? But this will just restrain the distance between COM of the 2 groups to the initial distance, but cannot restrain the conformation of the loop. Or need I divide the loop into many small segments (pull-groups) and define the pull coordinates separately? This seems horrible... You should probably be looking at a more advanced, multi-dimensional bias or collective variable. Look into PLUMED. GROMACS is going to be limited to a linear reaction coordinate, which may not capture everything you need in such a large transition. -Justin Thanks, Qing At 2017-04-08 09:06:46, "Justin Lemkul" wrote: On 4/7/17 8:56 PM, Qing Lv wrote: Dear Colleagues, I am trying to do an umbrella sampling using a series of conformations extracted from several unbiased MD trajectories. But I am not sure about the pull code in .mdp file. Below is the pull code from the tutorial of Dr. Justin Lemkul : define = -DPOSRES_B ; (Why ??) Did you read the paper I linked from the tutorial, which explains why this is done for this very specific case? ; Pull code pull= yes pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= Chain_B pull_group2_name= Chain_A pull_coord1_type= umbrella ; harmonic biasing force pull_coord1_geometry= distance ; simple distance increase pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_coord1_rate= 0.0 pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 Conformations in Justin's tutorial are from steered MD. However, my conformations are not from SMD, and I have not done SMD on this system. So, how to define pull_group1 and pull_group2? And pull_coord1_geometry still set to "distance" ? The pull groups don't depend on where the configurations came from. They define the reaction coordinate. You can use whatever pull geometry makes sense; in the tutorial it is a simple linear reaction coordinate directly along the z-axis. Other applications may require different definitions. Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES ") ? Why? Generally, no, but you haven't given any useful detail about what your simulation system is. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] BOND DISSOCIATION ENERGY STUDY USING GROMACS
On 4/8/17 2:49 AM, Neha Gupta wrote: Hi gromacs users, I want to calculate bond dissociation energy of a particular bond in my organic compound. How to proceed further? Can anyone let me know? This is a quantum mechanical calculation. Use an appropriate QM program, no GROMACS. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to heat atoms within a given region and obtain temperture profile
Hi, GROMACS users! I have looked through Gromacs manual. But I didn't find how to simulate thermal conductivity by NEMD method. The first problem is how to get a hot region and a cold region by thermostating atoms within a region. In addition, which gmx program could generate data of temperature profile along one direction? As to the first problem, I know it may need dynamic groups because atoms within a given region will change with time. Does Gromacs support thermostating dynamic groups and which gmx program is responsible for setting those groups? I found gmx select is usualy used for analysis but might not be for this usage. Could anyone give me some suggestions? Thank you very much! Sincerely, Chibang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] TOPOLBUILD
Hi gromacs users, I am using topolbuild to generate oplsaa force field parameters. ./topolbuild -n LIGAND.mol2 -dir C:/cygwin64/usr/local/gromacs/share/gromacs/top/oplsaa.ff -meas Need correct parameters . What should I do to get correct parameters? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to heat atoms within a given region and obtain temperture profile
Hi, GROMACS users! I have looked through Gromacs manual. But I didn't find how to simulate thermal conductivity by NEMD method. The first problem is how to get a hot region and a cold region by thermostating atoms within a region. In addition, which gmx program could generate data of temperature profile along one direction? As to the first problem, I know it may need dynamic groups because atoms within a given region will change with time. Does Gromacs support thermostating dynamic groups and which gmx program is responsible for setting those groups? I found gmx select is usualy used for analysis but might not be for this usage. Could anyone give me some suggestions? Thank you very much! Sincerely, Chibang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
