[gmx-users] Size of Water Pools
Hi All, I am simulating systems with lipids, water and surfactants. I observed formation of water pools/water aggregates with different sizes in final frames. Now I want to measure size of these pools. What gromacs tool do you suggest me to use? I tried to do clustering first and thought calculating radius of gyration. However, clustering process takes ages to complete. Could you please help me to determine size of these water pools? Thank you. -- Best Regards Shan Jayasinghe -- 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] Micellar shape
Thank you very much. On Wed, Feb 5, 2020 at 11:14 PM Justin Lemkul wrote: > > > On 2/5/20 12:01 AM, Shan Jayasinghe wrote: > > Dear Gromacs Users, > > > > I want to determine whether I got prolate or oblate micelle in my MD > > simulation. I calculated moment of inertia for a micelle after doing > > clustering. I want to know how do I determine whether it is prolate or > > oblate depending on moment of inertia calculations. > > Compute the ellipticity. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- Best Regards Shan Jayasinghe -- 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] Micellar shape
Dear Gromacs Users, I want to determine whether I got prolate or oblate micelle in my MD simulation. I calculated moment of inertia for a micelle after doing clustering. I want to know how do I determine whether it is prolate or oblate depending on moment of inertia calculations. Thank you. -- Best Regards Shan Jayasinghe -- 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] Make index command in gromacs
Dear Gromacs Users, Thank you very much for your valuable answers. On Wed, Jan 8, 2020 at 8:40 PM Christian Blau wrote: > Hi Shan, > > > gmx select gives you many more options to do complex arithmetic with > selections that might help you here. > > > You can try using > > gmx select -select "SELECTION STING" > > you'll find lots of selection string examples at the bottom in here: > > http://manual.gromacs.org/documentation/current/onlinehelp/selections.html > > > > Best, > > Christian > > > On 2020-01-07 23:33, Shan Jayasinghe wrote: > > Dear Gromacs Users, > > > > In my simulations, I have different sizes of water droplets. I need > > indexes of water molecules in each droplet separately. I am trying to > make > > the index file with gmx make_ndx, but I couldn't do it. Appreciate your > > help regarding this matter. > > > > Thank you. > -- > 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. > -- Best Regards Shan Jayasinghe -- 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] Make index command in gromacs
Dear Gromacs Users, In my simulations, I have different sizes of water droplets. I need indexes of water molecules in each droplet separately. I am trying to make the index file with gmx make_ndx, but I couldn't do it. Appreciate your help regarding this matter. Thank you. -- Best Regards Shan Jayasinghe -- 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] Chain length of a polymer
Dear Gromacs Users, I have a polymer molecule in my MD simulation and I want to calculate how chain length varies with simulation time. How can I do that with Gromacs software? Can I use gmx distance? Do I need to create a group with backbone atoms of the polymer chain in the index file for the calculation? Appreciate your help. Thank you. -- Best Regards Shan Jayasinghe -- 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] Coarse-grained MD
Dear Gromacs Users, I have surfactant and triglyceride united atom models which I used to do MD simulations with Gromacs. Now I want to do coarse grained MD simulations for the same systems using Gromacs. Appreciate, if anyone can guide me to setup the coarse grained simulation. Thank you. -- Best Regards Shan Jayasinghe -- 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] Ramachandran Plot for a Polymer
Dear Gromacs Users, Can we get the Ramachandran plot for a polymer using Gromacs? If we can, how do we do that? Appreciate your help. Thank you. -- Best Regards Shan Jayasinghe -- 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] Topology
Dear Gromacs Users, My molecule has a chiral center and I have topology for that configuration. I would like to know how do we get the topology for the opposite configuration in gromacs? Thank you. -- Best Regards Shan Jayasinghe -- 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] Potential Energy Distribution Plots in REMD
Dear Gromacs Users, I want to plot potential energy distribution plot using the normal distribution curve (bell curve) for all replicas in my REMD simulation. I used the command, gmx analyze -f Penergy.xvg -dist -normalize However, I got a histogram, instead of a bell curve. Appreciate, if you could help me to get the normalised curve for potential energy distribution. Thank you. -- Best Regards Shan Jayasinghe -- 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] SASA calculation for one replica in REMD
Dear Gromacs Users, Thank you for all suggestions. Yes I can use gmx SASA, but I want to know how do we use that in REMD simulations? Specifically, I want to calculate SASA for molecules in my first replica (298 K). But I think the trajectory in the first replica contains the information regarding to temperature exchanges. However, I want to calculate SASA for specifically at 298 K. How can we extract information only for 298 K. Thank you for any help that you can provide. On Tue, Apr 23, 2019 at 7:38 PM Tasneem Kausar wrote: > Check gmx sasa -h > It is implemented in Gromacs > > On Tue, Apr 23, 2019 at 2:37 PM Shan Jayasinghe < > shanjayasinghe2...@gmail.com> wrote: > > > Dear Gromacs Users, > > > > I did replica exchange molecular dynamics simulation which contains 25 > > replicas. Now I want to calculate the solvent accessible surface area of > > the surfactant (the first replica in my REMD) I used in my simulation at > > 298 K. How can I do that? > > > > Can anyone help me? > > > > Thank you. > > -- > > 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/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. > -- Best Regards Shan Jayasinghe -- 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] SASA calculation for one replica in REMD
Dear Gromacs Users, I did replica exchange molecular dynamics simulation which contains 25 replicas. Now I want to calculate the solvent accessible surface area of the surfactant (the first replica in my REMD) I used in my simulation at 298 K. How can I do that? Can anyone help me? Thank you. -- 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] Extending MD simulation
Dear Gromacs Users, Initially, I did my simulation for 50 ns using Gromacs 2016.3 version and now I want to extend my simulation for another 50 ns. At the same time I want to change output control parameters (nstxout and nstxtcout) in the mdp file. I would like to know two things. 1) What parameters do I need to change in the mdp file to continue the simulation from 50 ns? 2) How do I use grompp and mdrun commands to continue the MD simulation? Can anyone help me? Thank you. -- 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] Simulated Annealing
Dear Gromacs Users, How do we extend a simulated annealing? Thank you. Best Regards Shan Jayasinghe -- 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] Simulated Annealing
Dear Prof. Justin, Thank you very much for the answer. It is really helpful. On Tue, Feb 5, 2019 at 1:48 AM Justin Lemkul wrote: > > > On 2/1/19 4:45 PM, Shan Jayasinghe wrote: > > Dear Gromacs Users, > > > > I did a simulated annealing for my system and now I want to analyse my > > data. Can anyone suggest me a tutorial for this? What type of information > > we can get from simulated annealing? > > Usually annealing is just applied during equilibration to slowly change > the temperature of the system. Whether or not it's actually beneficial > is debatable. The temperature changes so quickly that you don't actually > sample any sort of thermodynamic equilibrium at any given temperature, > so there's no really useful analysis that I can think of. > > > I want to know whether the generated .gro file corresponds to the last > > temperature we defined in mdp file? > > The final coordinate file written by mdrun always corresponds to the > final frame, regardless of input settings. It may or may not correspond > to a state at exactly the temperature specified in the .mdp file. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- Best Regards Shan Jayasinghe -- 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] Simulated Annealing
Dear Gromacs Users, I did a simulated annealing for my system and now I want to analyse my data. Can anyone suggest me a tutorial for this? What type of information we can get from simulated annealing? I want to know whether the generated .gro file corresponds to the last temperature we defined in mdp file? Thank you. -- Best Regards Shan Jayasinghe -- 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] REMD Plots
Hi Joel, Thank you very much. On Wed, Jan 9, 2019 at 3:27 PM Joel Awuah wrote: > Hi Shan, > I am not quite sure if you want to generate an REMD simulation mobility in > temperature space for the 30 replicas. If that be the case, then you can > use the data in the replica_temperature.xvg file to plot replica index vs > REMD steps. The 1st column in the file corresponds to the REMD steps and > 2nd to 31st correspond to the mobility of replicas 0 to 29. > > Hope this helps? > > cheers > Joel > > > On Wed, 9 Jan 2019 at 13:23, Shan Jayasinghe > > wrote: > > > Dear Gromacs users, > > > > How do we plot a graph for temperature vs swap step number using a REMD > > simulation with 30 systems. I already generated the replica_temp.xvg and > > replica_index.xvg files using demux.pl script. > > > > Thank you. > > > > Best Regards > > Shan Jayasinghe > > -- > > 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. > > > > > -- > Joel Baffour Awuah > PhD Candidate > *Institute for Frontier Materials* > > *Deakin University* > *Waurn Ponds, 3126 VIC* > *Australia +61450070635* > -- > 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. > -- Best Regards Shan Jayasinghe -- 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] REMD Plots
Dear Gromacs users, How do we plot a graph for temperature vs swap step number using a REMD simulation with 30 systems. I already generated the replica_temp.xvg and replica_index.xvg files using demux.pl script. Thank you. Best Regards Shan Jayasinghe -- 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] Epsilon_r
Hi Justin, Thank you very much. On Tue, Dec 18, 2018 at 12:23 AM Justin Lemkul wrote: > On Mon, Dec 17, 2018 at 1:49 AM Shan Jayasinghe < > shanjayasinghe2...@gmail.com> wrote: > > > Dear Gromacs Users, > > > > How do we determine the epsilon_r for a MD simulation? If we do a MD > > simulation for a system with some molecules in water, what is the value > for > > epsilon_r? Is it equal to the relative dielectric permittivity of water? > > > > It is vacuum permittivity. Don't change it. > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2004-March/009650.html > > -Justin > > -- > > == > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > > == > -- > 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. > -- Best Regards Shan Jayasinghe -- 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] Epsilon_r
Dear Gromacs Users, How do we determine the epsilon_r for a MD simulation? If we do a MD simulation for a system with some molecules in water, what is the value for epsilon_r? Is it equal to the relative dielectric permittivity of water? Thank you. -- 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] gmx select with coordinates
Hi Prof. Dan, Thank you very much for the e-mail. How do we define coordinates what we want in VMD Graphical Representation menu? Thank you. On Wed, Oct 10, 2018 at 6:53 AM Dan Gil wrote: > Hi Shan, > > Sorry it's been a while - I don't check this email too often. Did you > figure the problem out? > > I use the Graphical Representations menu of VMD, although I am sure there > is a way to do it in the console too. > > On Thu, Sep 27, 2018 at 9:35 PM Shan Jayasinghe < > shanjayasinghe2...@gmail.com> wrote: > > > Dear Prof. Dan, > > > > Thank you very much for the suggestion. However, when I gave the command; > > gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx in > > VMD TkConsole, I didn't get any output. > > > > I didn't get the cursor in next line to type x > 45 and x < 90 and y > 90 > > and y. What could be the reason for this? Appreciate, if you can reply > me. > > > > Thank you. > > > > On Fri, Sep 28, 2018 at 12:00 AM Dan Gil wrote: > > > > > Hi, > > > > > > I believe you are trying to select atoms/particles that are in an > > > infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and > > > (90, 125)? > > > > > > Gmx select uses commands that are similar in syntax to a software > called > > > VMD. So I like to use VMD to figure out what I need to give to gmx > select > > > in order to get the selections I want. > > > > > > For example, I think for what you want, I would do: > > > > > > gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx > > > [Press Enter] > > > x > 45 and x < 90 and y > 90 and y < 125 [Press Enter] > > > > > > If you want to include it in a script without manual user input: > > > > > > echo x > 45 and x < 90 and y > 90 and y < 125 | gmx select -f run05.xtc > > -s > > > run05.tpr -b 39 -e 40 -on index.ndx > > > > > > VMD is great! It's also free software if you haven't tried using it > yet. > > > The only thing you gotta watch out for is that VMD uses Angstroms while > > GMX > > > uses nm. > > > > > > Dan > > > > > > On Thu, Sep 27, 2018 at 7:51 AM Shan Jayasinghe < > > > shanjayasinghe2...@gmail.com> wrote: > > > > > > > Dear Gromacs users, > > > > > > > > I want to make an index files with molecules in a particular area. I > > have > > > > four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] > > which > > > > define an area of the system. How can I do it with gmx_select? > > > > > > > > Can anyone help me? > > > > > > > > Thank you. > > > > > > > > On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe < > > > > shanjayasinghe2...@gmail.com> wrote: > > > > > > > > > > > > > > Dear Gromacs users, > > > > > > > > > > I want to make an index files with particular x and y coordinates. > > > There > > > > > is no restriction for z coordinates. How can I do it with > > gmx_select? I > > > > > already tried with the following command. However, it seems I don't > > get > > > > the > > > > > result I want. > > > > > > > > > > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f > > > > > run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx > > > > > > > > > > Can anyone help me? > > > > > > > > > > Thank you. > > > > > > > > > > > > > > > > > -- > > > > Best Regards > > > > Shan Jayasinghe > > > > -- > > > > 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/
[gmx-users] Pure-liquid MD Simulations
Dear Gromacs users, I am doing some MD simulations of pure-liquids. Depending on the pure compound we simulate, do we need to change the dielectric permittivity value in .mdp file? Thank you. -- 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] Global minimum
Dear Gromacs Users, How do we get the global minimum from a MD simulation? Is there any method available in Gromacs to reach global minimum structure rather than local minimum structures? Thank you. -- Best Regards Shan Jayasinghe -- 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] gmx select with coordinates
Dear Prof. Dan, Thank you very much for the suggestion. However, when I gave the command; gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx in VMD TkConsole, I didn't get any output. I didn't get the cursor in next line to type x > 45 and x < 90 and y > 90 and y. What could be the reason for this? Appreciate, if you can reply me. Thank you. On Fri, Sep 28, 2018 at 12:00 AM Dan Gil wrote: > Hi, > > I believe you are trying to select atoms/particles that are in an > infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and > (90, 125)? > > Gmx select uses commands that are similar in syntax to a software called > VMD. So I like to use VMD to figure out what I need to give to gmx select > in order to get the selections I want. > > For example, I think for what you want, I would do: > > gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx > [Press Enter] > x > 45 and x < 90 and y > 90 and y < 125 [Press Enter] > > If you want to include it in a script without manual user input: > > echo x > 45 and x < 90 and y > 90 and y < 125 | gmx select -f run05.xtc -s > run05.tpr -b 39 -e 40 -on index.ndx > > VMD is great! It's also free software if you haven't tried using it yet. > The only thing you gotta watch out for is that VMD uses Angstroms while GMX > uses nm. > > Dan > > On Thu, Sep 27, 2018 at 7:51 AM Shan Jayasinghe < > shanjayasinghe2...@gmail.com> wrote: > > > Dear Gromacs users, > > > > I want to make an index files with molecules in a particular area. I have > > four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] which > > define an area of the system. How can I do it with gmx_select? > > > > Can anyone help me? > > > > Thank you. > > > > On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe < > > shanjayasinghe2...@gmail.com> wrote: > > > > > > > > Dear Gromacs users, > > > > > > I want to make an index files with particular x and y coordinates. > There > > > is no restriction for z coordinates. How can I do it with gmx_select? I > > > already tried with the following command. However, it seems I don't get > > the > > > result I want. > > > > > > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f > > > run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx > > > > > > Can anyone help me? > > > > > > Thank you. > > > > > > > > > -- > > Best Regards > > Shan Jayasinghe > > -- > > 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/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. > -- Best Regards Shan Jayasinghe -- 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] gmx select with coordinates
Dear Gromacs users, I want to make an index files with molecules in a particular area. I have four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] which define an area of the system. How can I do it with gmx_select? Can anyone help me? Thank you. On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe < shanjayasinghe2...@gmail.com> wrote: > > Dear Gromacs users, > > I want to make an index files with particular x and y coordinates. There > is no restriction for z coordinates. How can I do it with gmx_select? I > already tried with the following command. However, it seems I don't get the > result I want. > > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f > run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx > > Can anyone help me? > > Thank you. > -- Best Regards Shan Jayasinghe -- 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] gmx select with coordinates
Dear Gromacs users, I want to make an index files with particular x and y coordinates. There is no restriction for z coordinates. How can I do it with gmx_select? I already tried with the following command. However, it seems I don't get the result I want. gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx Can anyone help me? Thank you. -- 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] Center to center distance in cylindrical micelles
Hi All, Does anyone know how to calculate distance between two adjacent cylinders in a hexagonal array? Thank you. On Sun, Aug 12, 2018 at 8:01 AM Shan Jayasinghe < shanjayasinghe2...@gmail.com> wrote: > Hi, > > Actually, I want to calculate the lattice parameter (distance between two > cylinders) of hexagonal phase. Appreciate, if you could help me. > > Thank you. > > > > > On Sat, Aug 11, 2018 at 11:11 PM Mark Abraham > wrote: > >> Hi, >> >> A center is a point. I don't see how you would define a central point of >> an >> infinite cylinder. >> >> Mark >> >> On Sat, Aug 11, 2018, 14:47 Shan Jayasinghe > > >> wrote: >> >> > Hi, >> > >> > I'm sorry for not providing the detail description of my system. >> Actually >> > it is a hexagonal phase. Therefore, four cylindrical micelles can be >> seen >> > in a cell. I want to calculate the center to center distance of two >> > cylindrical micelles. >> > >> > On Sat, Aug 11, 2018 at 8:35 PM Mark Abraham >> > wrote: >> > >> > > Hi, >> > > >> > > There is an axis of each cylinder but the two won't be parallel so >> there >> > is >> > > no unique distance to measure. So I suggest thinking carefully about >> what >> > > you really want. >> > > >> > > Mark >> > > >> > > On Sat, Aug 11, 2018, 06:58 Shan Jayasinghe < >> > shanjayasinghe2...@gmail.com> >> > > wrote: >> > > >> > > > Hi, >> > > > >> > > > I tried to used gmx distance. However, I don't understand how can I >> > > define >> > > > the center of the circle face of the cylinder to the same in the >> other >> > > > cylindrical micelle. >> > > > >> > > > Can anyone help me? >> > > > Thank you. >> > > > >> > > > >> > > > On Sat, Aug 11, 2018 at 9:33 AM Mark Abraham < >> mark.j.abra...@gmail.com >> > > >> > > > wrote: >> > > > >> > > > > Hi, >> > > > > >> > > > > Have you looked at the different tools available and considered >> what >> > > > might >> > > > > be useful for you? >> > > > > >> > > > > Mark >> > > > > >> > > > > On Fri, Aug 10, 2018, 07:34 Shan Jayasinghe < >> > > > shanjayasinghe2...@gmail.com> >> > > > > wrote: >> > > > > >> > > > > > Dear Gromacs Users, >> > > > > > >> > > > > > I want to calculate the center to center distance of two >> > cylindrical >> > > > > > micelles in my simulation. What gmx command should I use to >> > calculate >> > > > the >> > > > > > distance? Can anyone help me? >> > > > > > >> > > > > > Thank you. >> > > > > > -- >> > > > > > 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/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. >> > > > &g
Re: [gmx-users] Center to center distance in cylindrical micelles
Hi, Actually, I want to calculate the lattice parameter (distance between two cylinders) of hexagonal phase. Appreciate, if you could help me. Thank you. On Sat, Aug 11, 2018 at 11:11 PM Mark Abraham wrote: > Hi, > > A center is a point. I don't see how you would define a central point of an > infinite cylinder. > > Mark > > On Sat, Aug 11, 2018, 14:47 Shan Jayasinghe > wrote: > > > Hi, > > > > I'm sorry for not providing the detail description of my system. Actually > > it is a hexagonal phase. Therefore, four cylindrical micelles can be seen > > in a cell. I want to calculate the center to center distance of two > > cylindrical micelles. > > > > On Sat, Aug 11, 2018 at 8:35 PM Mark Abraham > > wrote: > > > > > Hi, > > > > > > There is an axis of each cylinder but the two won't be parallel so > there > > is > > > no unique distance to measure. So I suggest thinking carefully about > what > > > you really want. > > > > > > Mark > > > > > > On Sat, Aug 11, 2018, 06:58 Shan Jayasinghe < > > shanjayasinghe2...@gmail.com> > > > wrote: > > > > > > > Hi, > > > > > > > > I tried to used gmx distance. However, I don't understand how can I > > > define > > > > the center of the circle face of the cylinder to the same in the > other > > > > cylindrical micelle. > > > > > > > > Can anyone help me? > > > > Thank you. > > > > > > > > > > > > On Sat, Aug 11, 2018 at 9:33 AM Mark Abraham < > mark.j.abra...@gmail.com > > > > > > > wrote: > > > > > > > > > Hi, > > > > > > > > > > Have you looked at the different tools available and considered > what > > > > might > > > > > be useful for you? > > > > > > > > > > Mark > > > > > > > > > > On Fri, Aug 10, 2018, 07:34 Shan Jayasinghe < > > > > shanjayasinghe2...@gmail.com> > > > > > wrote: > > > > > > > > > > > Dear Gromacs Users, > > > > > > > > > > > > I want to calculate the center to center distance of two > > cylindrical > > > > > > micelles in my simulation. What gmx command should I use to > > calculate > > > > the > > > > > > distance? Can anyone help me? > > > > > > > > > > > > Thank you. > > > > > > -- > > > > > > 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/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. > > > > > > > > > > > > > > > > > -- > > > > Best Regards > > > > Shan Jayasinghe > > > > -- > > > > 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. > &g
Re: [gmx-users] Center to center distance in cylindrical micelles
Hi, I'm sorry for not providing the detail description of my system. Actually it is a hexagonal phase. Therefore, four cylindrical micelles can be seen in a cell. I want to calculate the center to center distance of two cylindrical micelles. On Sat, Aug 11, 2018 at 8:35 PM Mark Abraham wrote: > Hi, > > There is an axis of each cylinder but the two won't be parallel so there is > no unique distance to measure. So I suggest thinking carefully about what > you really want. > > Mark > > On Sat, Aug 11, 2018, 06:58 Shan Jayasinghe > wrote: > > > Hi, > > > > I tried to used gmx distance. However, I don't understand how can I > define > > the center of the circle face of the cylinder to the same in the other > > cylindrical micelle. > > > > Can anyone help me? > > Thank you. > > > > > > On Sat, Aug 11, 2018 at 9:33 AM Mark Abraham > > wrote: > > > > > Hi, > > > > > > Have you looked at the different tools available and considered what > > might > > > be useful for you? > > > > > > Mark > > > > > > On Fri, Aug 10, 2018, 07:34 Shan Jayasinghe < > > shanjayasinghe2...@gmail.com> > > > wrote: > > > > > > > Dear Gromacs Users, > > > > > > > > I want to calculate the center to center distance of two cylindrical > > > > micelles in my simulation. What gmx command should I use to calculate > > the > > > > distance? Can anyone help me? > > > > > > > > Thank you. > > > > -- > > > > 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/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. > > > > > > > > > -- > > Best Regards > > Shan Jayasinghe > > -- > > 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/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. > -- Best Regards Shan Jayasinghe -- 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] Center to center distance in cylindrical micelles
Hi, I tried to used gmx distance. However, I don't understand how can I define the center of the circle face of the cylinder to the same in the other cylindrical micelle. Can anyone help me? Thank you. On Sat, Aug 11, 2018 at 9:33 AM Mark Abraham wrote: > Hi, > > Have you looked at the different tools available and considered what might > be useful for you? > > Mark > > On Fri, Aug 10, 2018, 07:34 Shan Jayasinghe > wrote: > > > Dear Gromacs Users, > > > > I want to calculate the center to center distance of two cylindrical > > micelles in my simulation. What gmx command should I use to calculate the > > distance? Can anyone help me? > > > > Thank you. > > -- > > 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/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. > -- Best Regards Shan Jayasinghe -- 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] Center to center distance in cylindrical micelles
Dear Gromacs Users, I want to calculate the center to center distance of two cylindrical micelles in my simulation. What gmx command should I use to calculate the distance? Can anyone help me? Thank you. -- 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.
