Re: [gmx-users] velocity
Maybe you checked .xtc file Velocity is in .trr file Quyen V. Vu Web frontend developer On Mon, May 28, 2018, 18:42 Mark Abraham wrote: > Hi, > > Only if you asked for velocity information to be written to the trajectory, > with nstvout > > Mark > > On Mon, May 28, 2018 at 1:06 PM Atila Petrosian > > wrote: > > > Dear gromacs users, > > > > I did md simulation. I need to velocity values for each atoms in time > > steps. > > > > Can I get this parameter from trajectory file directly? > > > > How to obtain that? > > > > 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. > > > -- > 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.
[gmx-users] velocity
Dear Mark and Justin, My problem was solved using trr file. Thanks for guidance. -- 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] velocity
Hi, An xtc file only contains positions. Your nstvout affects the trr file. Notice how sharing your command line got you the answer you needed ;-) Mark On Mon, May 28, 2018, 18:12 Atila Petrosian wrote: > Dear Justin, > > In my last md simulation, I used > > nstxout = 1000 > nstvout = 1000 > nstxtcout = 1000 > nstenergy = 1000 > nstlog = 1000 > > After your suggestion, I used gmx traj -f npt.xtc -s npt.tpr -ov veloc.xvg > -n index.ndx > > veloc.xvg file is as follows: > > - > > @title "Velocity" > @xaxis label "Time (ps)" > @yaxis label "Velocity (nm/ps)" > @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 "atom 1 X" > @ s1 legend "atom 1 Y" > @ s2 legend "atom 1 Z" > . > . > . > @ s2838 legend "atom 947 X" > @ s2839 legend "atom 947 Y" > @ s2840 legend "atom 947 Z"*** (last line of file) *** > > -- > > There is no velocity values. Is my manner wrong? > -- > 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.
[gmx-users] velocity
Dear Justin, In my last md simulation, I used nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstenergy = 1000 nstlog = 1000 After your suggestion, I used gmx traj -f npt.xtc -s npt.tpr -ov veloc.xvg -n index.ndx veloc.xvg file is as follows: - @title "Velocity" @xaxis label "Time (ps)" @yaxis label "Velocity (nm/ps)" @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 "atom 1 X" @ s1 legend "atom 1 Y" @ s2 legend "atom 1 Z" . . . @ s2838 legend "atom 947 X" @ s2839 legend "atom 947 Y" @ s2840 legend "atom 947 Z"*** (last line of file) *** -- There is no velocity values. Is my manner wrong? -- 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] velocity
On 5/28/18 11:49 AM, Atila Petrosian wrote: Dear Mark, Thanks for your answer. "Only if you asked for velocity information to be written to the trajectory, with nstvout" Usually, I use the following lines in mdp files: nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstenergy = 1000 nstlog = 1000 But, I get only position of atoms in time steps using VMD while I need to the velocity values for each time in time steps. Inspect the contents of your .trr file to verify what you have (is what you "usually" do what you "always" do, or did you forget something in this case?) and then, if velocities are present, extract what you need with gmx traj. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 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.
[gmx-users] velocity
Dear Mark, Thanks for your answer. "Only if you asked for velocity information to be written to the trajectory, with nstvout" Usually, I use the following lines in mdp files: nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstenergy = 1000 nstlog = 1000 But, I get only position of atoms in time steps using VMD while I need to the velocity values for each time in time steps. -- 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] velocity
Hi, Only if you asked for velocity information to be written to the trajectory, with nstvout Mark On Mon, May 28, 2018 at 1:06 PM Atila Petrosian wrote: > Dear gromacs users, > > I did md simulation. I need to velocity values for each atoms in time > steps. > > Can I get this parameter from trajectory file directly? > > How to obtain that? > > 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. > -- 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] velocity
Dear gromacs users, I did md simulation. I need to velocity values for each atoms in time steps. Can I get this parameter from trajectory file directly? How to obtain that? 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.
[gmx-users] velocity profile in nanochannel flows
Hi all, Is anyone familiar with any method to calculate velocity profile in a nanochannel flow? Best Regards -- 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] Velocity as a function of distance Z
On Fri, Mar 3, 2017 at 11:50 AM Kamps, M. wrote: > (previous mail was sent prematurely, my apologies) > > Dear Mark, > > Again, thanks for the reply. > > You said I should identify groups of molecules that are to my > interest. I'm unsure how to do this. > My .gro files show no distinction between different molecules, all of > them are built the same (rows deleted for clarification). > > 1EthBC1 5963 18.910 0.037 2.874 0.4243 0.6722 -0.0361 > 1EthB H11 5964 18.969 0.099 2.810 1.4488 0.2545 0.0251 > ... > 5EthH21 5992 18.287 0.495 3.423 0.1969 0.2998 0.4129 > 5EthH22 5993 18.291 0.508 3.251 0.7485 -2.7065 0.0733 > ... >10EthE H22 6023 17.188 0.735 3.427 -0.4008 -2.3617 0.5620 >10EthE H23 6024 17.153 0.699 3.263 2.2014 0.6628 -1.8300 > > What should I enter to select individual molecules? There are no > columns or names that are unique to a single molecule? > Here, residue numbers 1-10 look like a molecule. If so, then residue 11-20 might be a second one, etc. So you can set up some groups via something like molecule1 = resindex 1 to 10; molecule2 = resindex 11 to 20; etc. Perhaps needing a script to generate that, to re-use a bunch of times. Perhaps, if given a .tpr, we could extend the selection syntax to be aware of molecules. In the 'Selection syntax and usage' document there are tons of > options, however I find it difficult to know which one to use, and how > to use them. > First, make sure you can write a sentence that completely describes how you want to select things, e.g. from the frame at time x I want a set of index groups, with each group a single molecule, whose center of mass has a z coordinate between n and m. Then work out how to express that, e.g by starting to work out how to select a single molecule based on http://manual.gromacs.org/documentation/2016.2/user-guide/cmdline.html#selection-syntax-and-usage. Just guessing at syntax doesn't help you work out what you actually want :-) > The distinctions that I can make are in their residue > (EthB-(Eth)n-EthE), which will select all atoms in these groups, > instead of whole molecules. I could also make a selection based on > their position, however that would mean not entire molecules are > taken. When i say for example resname EthB EthE Eth and x>5 and x<7, > all atoms inside this margin will be taken, however this would mean it > will select partial/split/cut molecules, since parts of the molecule > will be outside of this frame. When looking at the earlier mentioned > document, I see for example the 'chain' option. But I can't figure out > how to use this. > So maybe molecule1 and com of molecule1 (z > 11 or z < 13) I'm no expert on the selection syntax, since I've never used it to solve a serious problem, so do start a new thread if you can't find something that works. Mark My residue groups are defined via residuetypes.dat to be: > EthPolymer > EthBPolymer > EthEPolymer > While in my topology they are called simply: > C20H42 > C16H34 > Is this helpful to make a molecule selection? > > > Mark > > -- 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] Velocity as a function of distance Z
(previous mail was sent prematurely, my apologies) Dear Mark, Again, thanks for the reply. You said I should identify groups of molecules that are to my interest. I'm unsure how to do this. My .gro files show no distinction between different molecules, all of them are built the same (rows deleted for clarification). 1EthBC1 5963 18.910 0.037 2.874 0.4243 0.6722 -0.0361 1EthB H11 5964 18.969 0.099 2.810 1.4488 0.2545 0.0251 ... 5EthH21 5992 18.287 0.495 3.423 0.1969 0.2998 0.4129 5EthH22 5993 18.291 0.508 3.251 0.7485 -2.7065 0.0733 ... 10EthE H22 6023 17.188 0.735 3.427 -0.4008 -2.3617 0.5620 10EthE H23 6024 17.153 0.699 3.263 2.2014 0.6628 -1.8300 What should I enter to select individual molecules? There are no columns or names that are unique to a single molecule? In the 'Selection syntax and usage' document there are tons of options, however I find it difficult to know which one to use, and how to use them. The distinctions that I can make are in their residue (EthB-(Eth)n-EthE), which will select all atoms in these groups, instead of whole molecules. I could also make a selection based on their position, however that would mean not entire molecules are taken. When i say for example resname EthB EthE Eth and x>5 and x<7, all atoms inside this margin will be taken, however this would mean it will select partial/split/cut molecules, since parts of the molecule will be outside of this frame. When looking at the earlier mentioned document, I see for example the 'chain' option. But I can't figure out how to use this. My residue groups are defined via residuetypes.dat to be: EthPolymer EthBPolymer EthEPolymer While in my topology they are called simply: C20H42 C16H34 Is this helpful to make a molecule selection? Mark >>> Dear Mark, >>> >>> Thanks again for your reply. I'm sorry for asking these probably >>> stupid questions, but I'm not able to figure it out. >>> >>> The objects I am interested in are small polymers, consisting of three >>> residue groups; Eth EthE and EthB (corresponding to both the end >>> groups of a polymer, and the middle section). I total these groups >>> consist of around 25000 atoms. >>> >> >> Those names won't help you. You want to identify (groups of) single >> molecules. Look at your file and see what distinguishes them. >> >>> With gmx select I will enter the following command, at an arbitrarily >>> chosen time: >>> gmx select -f input.trr -s input.tpr -on output.ndx -b 7.5 -e 7.5 >>> In the following selection screen my preferred molecules are listed as >>> three different groups (Eth, EthE and EthB), therefore I manually >>> select these groups with the command: resname Eth EthE EthB, press >>> enter and end with Ctrl-D. It will then proceed to process the frames, >>> where GROMACS tells me it has analyzed 1 frame, at the 30th timestep, >>> which is 7.5. >>> >> >> I can't see everything, but probably all you did was select every atom, >> which won't help you. You wanted all the molecules with some criterion, so >> you will need to make a better selection. >> >>> I will then switch to gmx traj where I enter the following: >>> gmx traj -f input.trr -s input.tpr -n output.ndx -ov output.xvg >>> It will then process all frames, and not only the frame I selected >>> during gmx select. Do I need to specify -b and -e again during gmx >>> traj? >>> >> >> Yes, once you've made a selection that matches geometric criteria from a >> frame, it is literally only applicable to that frame. >> >>> Then, the output could be read with xmgrace, however looking at the >>> files it will try to plot 25000 different lines, which it probably >>> cant. Opening the .xvg file plots the velocity/time plot of only 1 >>> atom, while opening the .xvg file for the time selected output (via >>> gmx traj -b -e) shows an empty plot for only one atom. >>> >> >> You haven't selected eg one molecule from one frame yet, so get that right >> first. >> >> Mark >> >>> I'm getting lost in all the options, any help would be appreciated. >>> >>> Mark >>> -- 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] Velocity as a function of distance Z (Mark Abraham)
Hi, On Wed, 1 Mar 2017 14:11 Kamps, M. wrote: Dear Mark, Thanks again for your reply. I'm sorry for asking these probably stupid questions, but I'm not able to figure it out. The objects I am interested in are small polymers, consisting of three residue groups; Eth EthE and EthB (corresponding to both the end groups of a polymer, and the middle section). I total these groups consist of around 25000 atoms. Those names won't help you. You want to identify (groups of) single molecules. Look at your file and see what distinguishes them. With gmx select I will enter the following command, at an arbitrarily chosen time: gmx select -f input.trr -s input.tpr -on output.ndx -b 7.5 -e 7.5 In the following selection screen my preferred molecules are listed as three different groups (Eth, EthE and EthB), therefore I manually select these groups with the command: resname Eth EthE EthB, press enter and end with Ctrl-D. It will then proceed to process the frames, where GROMACS tells me it has analyzed 1 frame, at the 30th timestep, which is 7.5. I can't see everything, but probably all you did was select every atom, which won't help you. You wanted all the molecules with some criterion, so you will need to make a better selection. I will then switch to gmx traj where I enter the following: gmx traj -f input.trr -s input.tpr -n output.ndx -ov output.xvg It will then process all frames, and not only the frame I selected during gmx select. Do I need to specify -b and -e again during gmx traj? Yes, once you've made a selection that matches geometric criteria from a frame, it is literally only applicable to that frame. Then, the output could be read with xmgrace, however looking at the files it will try to plot 25000 different lines, which it probably cant. Opening the .xvg file plots the velocity/time plot of only 1 atom, while opening the .xvg file for the time selected output (via gmx traj -b -e) shows an empty plot for only one atom. You haven't selected eg one molecule from one frame yet, so get that right first. Mark I'm getting lost in all the options, any help would be appreciated. Mark -- 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.
Re: [gmx-users] Velocity as a function of distance Z (Mark Abraham)
Dear Mark, Thanks again for your reply. I'm sorry for asking these probably stupid questions, but I'm not able to figure it out. The objects I am interested in are small polymers, consisting of three residue groups; Eth EthE and EthB (corresponding to both the end groups of a polymer, and the middle section). I total these groups consist of around 25000 atoms. With gmx select I will enter the following command, at an arbitrarily chosen time: gmx select -f input.trr -s input.tpr -on output.ndx -b 7.5 -e 7.5 In the following selection screen my preferred molecules are listed as three different groups (Eth, EthE and EthB), therefore I manually select these groups with the command: resname Eth EthE EthB, press enter and end with Ctrl-D. It will then proceed to process the frames, where GROMACS tells me it has analyzed 1 frame, at the 30th timestep, which is 7.5. I will then switch to gmx traj where I enter the following: gmx traj -f input.trr -s input.tpr -n output.ndx -ov output.xvg It will then process all frames, and not only the frame I selected during gmx select. Do I need to specify -b and -e again during gmx traj? Then, the output could be read with xmgrace, however looking at the files it will try to plot 25000 different lines, which it probably cant. Opening the .xvg file plots the velocity/time plot of only 1 atom, while opening the .xvg file for the time selected output (via gmx traj -b -e) shows an empty plot for only one atom. I'm getting lost in all the options, any help would be appreciated. Mark -- 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] Velocity as a function of distance Z
Hi, On Tue, Feb 28, 2017 at 11:55 AM Kamps, M. wrote: > Dear Mark, > > Thanks for your reply. Correct me if i'm wrong, but your suggestion > would be to determine the position of each atom/molecule during a > frame. This process should be repeated for each frame, which is > easiest to do with a manually written (non-GROMACS) script. > Yes. For each frame, call gmx select to make whatever groups suit you in an index file, then call gmx traj with that index file to produce things related to the velocities of the atoms in those groups. > With these positions per time, gmx traj should be able to determine > the velocity of each atom/molecule? If so, I will try to figure this > out. > Sure, that's what gmx traj -ov does, which is why I suggested you look at its help text. > Furthermore, is there a way to automatically select multiple atoms as > a molecule? My simulation uses small simple polymers, is there a way > to let GROMACS calculate only the positions or velocities of the > molecules instead of the atoms? > Generally, only by making an index group for that molecule. gmx select likely does everything you can imagine, and more. http://manual.gromacs.org/documentation/2016/onlinehelp/selections.html#specifying-selections-from-command-line Mark Mark > -- > 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.
Re: [gmx-users] Velocity as a function of distance Z
Dear Mark, Thanks for your reply. Correct me if i'm wrong, but your suggestion would be to determine the position of each atom/molecule during a frame. This process should be repeated for each frame, which is easiest to do with a manually written (non-GROMACS) script. With these positions per time, gmx traj should be able to determine the velocity of each atom/molecule? If so, I will try to figure this out. Furthermore, is there a way to automatically select multiple atoms as a molecule? My simulation uses small simple polymers, is there a way to let GROMACS calculate only the positions or velocities of the molecules instead of the atoms? Mark -- 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] Velocity as a function of distance Z
Hi, A group whose composition is defined geometrically over time requires constructing a dynamic selection, which is done with gmx select. Unfortunately that currently means writing a script to loop over frames, calling gmx select to make a suitable index file, then here e.g. gmx traj. Do check out gmx traj -h for useful options there. Mark On Mon, 27 Feb 2017 13:11 Kamps, M. wrote: Dear gmx-users, I have several simulations regarding atoms flowing between two gold surfaces. The flow of the liquid molecules show a distinct Poiseuille flow, which was expected. I am now interested in extracting the velocities of these liquid molecules (total of around 3 atoms, around 700 molecules). I am interested in the (average) velocity, as a function of the height Z. Is this possible in any way? If I take for example the command gmx traj ... -av, I will get the average velocity of all atoms, however I cannot tell which atom is placed where. Furthermore, is it possible to get the average velocities per molecule instead of atoms, for instance via gmx traj? Thanks in advance. Mark -- 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.
[gmx-users] Velocity as a function of distance Z
Dear gmx-users, I have several simulations regarding atoms flowing between two gold surfaces. The flow of the liquid molecules show a distinct Poiseuille flow, which was expected. I am now interested in extracting the velocities of these liquid molecules (total of around 3 atoms, around 700 molecules). I am interested in the (average) velocity, as a function of the height Z. Is this possible in any way? If I take for example the command gmx traj ... -av, I will get the average velocity of all atoms, however I cannot tell which atom is placed where. Furthermore, is it possible to get the average velocities per molecule instead of atoms, for instance via gmx traj? Thanks in advance. Mark -- 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] velocity generation in Gromacs 2016
On 1/24/17 10:42 AM, Kukol, Andreas wrote: Hello, I always used to generate velocities for an MD run in the equilibation step by setting gen-velyes in the mdp-file. In the sample mdp-file for Gromac 2016, this option is not set. Does it mean velocities are now generated by default ? http://manual.gromacs.org/documentation/2016.1/user-guide/file-formats.html#mdp The reason behind my question is, I actually forgot to set it and the MD-simulation seemed to run normally. The default is to not generate velocities, which has been the default for many years. http://manual.gromacs.org/documentation/2016.1/user-guide/mdp-options.html#velocity-generation So your simulation will start out at 0 K and the thermostat will try to bring it up to the correct temperature, unless the input coordinate file has velocities (e.g. in a .gro file). You can confirm what happened in the .log file, where the initial temperature is printed. -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] velocity generation in Gromacs 2016
Hello, I always used to generate velocities for an MD run in the equilibation step by setting gen-velyes in the mdp-file. In the sample mdp-file for Gromac 2016, this option is not set. Does it mean velocities are now generated by default ? http://manual.gromacs.org/documentation/2016.1/user-guide/file-formats.html#mdp The reason behind my question is, I actually forgot to set it and the MD-simulation seemed to run normally. Many thanks Andreas -- 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] velocity in trjconv
Hi, Probably you should use '-novel' On Mon, Oct 12, 2015 at 10:23 PM, Parvez Mh wrote: > Dear all, > I need to convert .trr file into .gro file without velocity. That's why i > used '-vel no' , but i got error 'invalid argument no'. Can any tell me how > to use -vel option for not writing velocity in .gro file . > > Regards > Masrul > -- > 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. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] velocity in trjconv
On 10/12/15 12:53 PM, Parvez Mh wrote: Dear all, I need to convert .trr file into .gro file without velocity. That's why i used '-vel no' , but i got error 'invalid argument no'. Can any tell me how to use -vel option for not writing velocity in .gro file . As with all GROMACS boolean options, the formation is -option/-nooption, so in this case specifically the proper syntax is -novel. -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] velocity in trjconv
Dear all, I need to convert .trr file into .gro file without velocity. That's why i used '-vel no' , but i got error 'invalid argument no'. Can any tell me how to use -vel option for not writing velocity in .gro file . Regards Masrul -- 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] Velocity Verlet integrator
Thank you very much for this reference. I will take a look at it carefully.
We are trying to develop and implement this integrators for hybrid Monte
Carlo simulations and our interest is not really related to time saving but
to sampling efficiency.
Right now it doesn't look straightforward to me to adapt GROMACS to this
integration schemes.
2014-10-15 17:05 GMT+02:00 Michael Shirts :
> Yes, I've been using the theory here:
>
> http://arxiv.org/abs/1301.3800
>
> Which describes how to concantenate integrator steps in a formal way.
>
> I can say that the time savings you get by concatenating integrators is
> VERY small. The only time it is nonnegligible is when there is a LOT of
> communication, and even then, there are better ways to make simulations
> faster. It's not an area where there is a lot of improvement that can be
> made.
>
> When doing temperature and pressure control, there are many cases that you
> cannot really join the steps as well.
>
> On Wed, Oct 15, 2014 at 10:05 AM, Mario Fernández Pendás <
> mariof...@gmail.com> wrote:
>
> > Thank you very much Professor Shirts.
> >
> > I have these doubts because I am trying to implement new integrators
> based
> > in the concatenation of two VV steps to make a single step. The idea
> > follows the integrators suggested in
> > http://web.mit.edu/~ripper/www/research/efficient_md_integrators.pdf
> >
> > This is why it is important for me to know where each step starts and
> > finishes.
> >
> > 2014-10-15 15:52 GMT+02:00 Michael Shirts :
> >
> > > Because the 'start' of the vv integrator step is halfway through the
> > loop.
> > > This is a byproduct of 1) putting leapfrog and velocity verlet in the
> > same
> > > loop and 2) minimizing communication and output. It is not as elegant
> as
> > > it should be. There are efforts to clean this up, but it's a lot of
> > > reorganization, and has gone slowly.
> > >
> > > On Wed, Oct 15, 2014 at 8:46 AM, Mario Fernández Pendás <
> > > mariof...@gmail.com
> > > > wrote:
> > >
> > > > Yes, I understand that. But my question is more about why the two
> > > velocity
> > > > updates are implemented before the position update and not the other
> > way
> > > > round?
> > > >
> > > > From the theoretical point of view I would think more in one of the
> > > > following schemes:
> > > >
> > > >
> > > >1. Calculate: [image: \vec{v}\left(t + \tfrac12\,\Delta t\right) =
> > > >\vec{v}(t) + \tfrac12\,\vec{a}(t)\,\Delta t\,]
> > > >2. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
> > > >\vec{v}\left(t + \tfrac12\,\Delta t\right)\, \Delta t\,]
> > > >3. Derive [image: \vec{a}(t + \Delta t)] from the interaction
> > > potential
> > > >using [image: \vec{x}(t + \Delta t)]
> > > >4. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}\left(t +
> > > >\tfrac12\,\Delta t\right) + \tfrac12\,\vec{a}(t + \Delta t)\Delta
> > t,]
> > > >
> > > >
> > > >
> > > >1. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
> > > \vec{v}(t)\,
> > > >\Delta t+\tfrac12 \,\vec{a}(t)\,\Delta t^2]
> > > >2. Derive [image: \vec{a}(t + \Delta t)] from the interaction
> > > potential
> > > >using [image: \vec{x}(t + \Delta t)]
> > > >3. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}(t) +
> > > >\tfrac12\,\left(\vec{a}(t)+\vec{a}(t + \Delta t)\right)\Delta t\,]
> > > >
> > > >
> > > > This is why my confusion arises.
> > > >
> > > >
> > > > 2014-10-15 14:05 GMT+02:00 Justin Lemkul :
> > > >
> > > > >
> > > > >
> > > > > On 10/15/14 7:30 AM, Mario Fernández Pendás wrote:
> > > > >
> > > > >> Dear all,
> > > > >>
> > > > >> I am still interested in some integrator related issues.
> > > > >>
> > > > >> I understand that the easiest way to implement velocity Verlet was
> > to
> > > > >> split
> > > > >> the updates in two updates. But I don't understad the order of
> those
> > > > >> updates.
> > > > >> I mean why there are two updates for velocities and then the
> update
> > > for
> > > > >> positions?
> > > > >> My intuitive idea would be to update first one half for
> velocities,
> > > > then a
> > > > >> full step for positions and, finally, using these new positions
> the
> > > > second
> > > > >> half for velocities.
> > > > >>
> > > > >
> > > > > Yes, there are two separate half-step updates for velocities. The
> > > > > comments in the md.cpp code are quite verbose if you want to trace
> > > > through.
> > > > >
> > > > > -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
> > > > >
> > > >
Re: [gmx-users] Velocity Verlet integrator
Yes, I've been using the theory here:
http://arxiv.org/abs/1301.3800
Which describes how to concantenate integrator steps in a formal way.
I can say that the time savings you get by concatenating integrators is
VERY small. The only time it is nonnegligible is when there is a LOT of
communication, and even then, there are better ways to make simulations
faster. It's not an area where there is a lot of improvement that can be
made.
When doing temperature and pressure control, there are many cases that you
cannot really join the steps as well.
On Wed, Oct 15, 2014 at 10:05 AM, Mario Fernández Pendás <
mariof...@gmail.com> wrote:
> Thank you very much Professor Shirts.
>
> I have these doubts because I am trying to implement new integrators based
> in the concatenation of two VV steps to make a single step. The idea
> follows the integrators suggested in
> http://web.mit.edu/~ripper/www/research/efficient_md_integrators.pdf
>
> This is why it is important for me to know where each step starts and
> finishes.
>
> 2014-10-15 15:52 GMT+02:00 Michael Shirts :
>
> > Because the 'start' of the vv integrator step is halfway through the
> loop.
> > This is a byproduct of 1) putting leapfrog and velocity verlet in the
> same
> > loop and 2) minimizing communication and output. It is not as elegant as
> > it should be. There are efforts to clean this up, but it's a lot of
> > reorganization, and has gone slowly.
> >
> > On Wed, Oct 15, 2014 at 8:46 AM, Mario Fernández Pendás <
> > mariof...@gmail.com
> > > wrote:
> >
> > > Yes, I understand that. But my question is more about why the two
> > velocity
> > > updates are implemented before the position update and not the other
> way
> > > round?
> > >
> > > From the theoretical point of view I would think more in one of the
> > > following schemes:
> > >
> > >
> > >1. Calculate: [image: \vec{v}\left(t + \tfrac12\,\Delta t\right) =
> > >\vec{v}(t) + \tfrac12\,\vec{a}(t)\,\Delta t\,]
> > >2. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
> > >\vec{v}\left(t + \tfrac12\,\Delta t\right)\, \Delta t\,]
> > >3. Derive [image: \vec{a}(t + \Delta t)] from the interaction
> > potential
> > >using [image: \vec{x}(t + \Delta t)]
> > >4. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}\left(t +
> > >\tfrac12\,\Delta t\right) + \tfrac12\,\vec{a}(t + \Delta t)\Delta
> t,]
> > >
> > >
> > >
> > >1. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
> > \vec{v}(t)\,
> > >\Delta t+\tfrac12 \,\vec{a}(t)\,\Delta t^2]
> > >2. Derive [image: \vec{a}(t + \Delta t)] from the interaction
> > potential
> > >using [image: \vec{x}(t + \Delta t)]
> > >3. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}(t) +
> > >\tfrac12\,\left(\vec{a}(t)+\vec{a}(t + \Delta t)\right)\Delta t\,]
> > >
> > >
> > > This is why my confusion arises.
> > >
> > >
> > > 2014-10-15 14:05 GMT+02:00 Justin Lemkul :
> > >
> > > >
> > > >
> > > > On 10/15/14 7:30 AM, Mario Fernández Pendás wrote:
> > > >
> > > >> Dear all,
> > > >>
> > > >> I am still interested in some integrator related issues.
> > > >>
> > > >> I understand that the easiest way to implement velocity Verlet was
> to
> > > >> split
> > > >> the updates in two updates. But I don't understad the order of those
> > > >> updates.
> > > >> I mean why there are two updates for velocities and then the update
> > for
> > > >> positions?
> > > >> My intuitive idea would be to update first one half for velocities,
> > > then a
> > > >> full step for positions and, finally, using these new positions the
> > > second
> > > >> half for velocities.
> > > >>
> > > >
> > > > Yes, there are two separate half-step updates for velocities. The
> > > > comments in the md.cpp code are quite verbose if you want to trace
> > > through.
> > > >
> > > > -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.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/
Re: [gmx-users] Velocity Verlet integrator
Thank you very much Professor Shirts.
I have these doubts because I am trying to implement new integrators based
in the concatenation of two VV steps to make a single step. The idea
follows the integrators suggested in
http://web.mit.edu/~ripper/www/research/efficient_md_integrators.pdf
This is why it is important for me to know where each step starts and
finishes.
2014-10-15 15:52 GMT+02:00 Michael Shirts :
> Because the 'start' of the vv integrator step is halfway through the loop.
> This is a byproduct of 1) putting leapfrog and velocity verlet in the same
> loop and 2) minimizing communication and output. It is not as elegant as
> it should be. There are efforts to clean this up, but it's a lot of
> reorganization, and has gone slowly.
>
> On Wed, Oct 15, 2014 at 8:46 AM, Mario Fernández Pendás <
> mariof...@gmail.com
> > wrote:
>
> > Yes, I understand that. But my question is more about why the two
> velocity
> > updates are implemented before the position update and not the other way
> > round?
> >
> > From the theoretical point of view I would think more in one of the
> > following schemes:
> >
> >
> >1. Calculate: [image: \vec{v}\left(t + \tfrac12\,\Delta t\right) =
> >\vec{v}(t) + \tfrac12\,\vec{a}(t)\,\Delta t\,]
> >2. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
> >\vec{v}\left(t + \tfrac12\,\Delta t\right)\, \Delta t\,]
> >3. Derive [image: \vec{a}(t + \Delta t)] from the interaction
> potential
> >using [image: \vec{x}(t + \Delta t)]
> >4. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}\left(t +
> >\tfrac12\,\Delta t\right) + \tfrac12\,\vec{a}(t + \Delta t)\Delta t,]
> >
> >
> >
> >1. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
> \vec{v}(t)\,
> >\Delta t+\tfrac12 \,\vec{a}(t)\,\Delta t^2]
> >2. Derive [image: \vec{a}(t + \Delta t)] from the interaction
> potential
> >using [image: \vec{x}(t + \Delta t)]
> >3. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}(t) +
> >\tfrac12\,\left(\vec{a}(t)+\vec{a}(t + \Delta t)\right)\Delta t\,]
> >
> >
> > This is why my confusion arises.
> >
> >
> > 2014-10-15 14:05 GMT+02:00 Justin Lemkul :
> >
> > >
> > >
> > > On 10/15/14 7:30 AM, Mario Fernández Pendás wrote:
> > >
> > >> Dear all,
> > >>
> > >> I am still interested in some integrator related issues.
> > >>
> > >> I understand that the easiest way to implement velocity Verlet was to
> > >> split
> > >> the updates in two updates. But I don't understad the order of those
> > >> updates.
> > >> I mean why there are two updates for velocities and then the update
> for
> > >> positions?
> > >> My intuitive idea would be to update first one half for velocities,
> > then a
> > >> full step for positions and, finally, using these new positions the
> > second
> > >> half for velocities.
> > >>
> > >
> > > Yes, there are two separate half-step updates for velocities. The
> > > comments in the md.cpp code are quite verbose if you want to trace
> > through.
> > >
> > > -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.
> > >
> > --
> > 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.
>
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Re: [gmx-users] Velocity Verlet integrator
Because the 'start' of the vv integrator step is halfway through the loop.
This is a byproduct of 1) putting leapfrog and velocity verlet in the same
loop and 2) minimizing communication and output. It is not as elegant as
it should be. There are efforts to clean this up, but it's a lot of
reorganization, and has gone slowly.
On Wed, Oct 15, 2014 at 8:46 AM, Mario Fernández Pendás wrote:
> Yes, I understand that. But my question is more about why the two velocity
> updates are implemented before the position update and not the other way
> round?
>
> From the theoretical point of view I would think more in one of the
> following schemes:
>
>
>1. Calculate: [image: \vec{v}\left(t + \tfrac12\,\Delta t\right) =
>\vec{v}(t) + \tfrac12\,\vec{a}(t)\,\Delta t\,]
>2. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
>\vec{v}\left(t + \tfrac12\,\Delta t\right)\, \Delta t\,]
>3. Derive [image: \vec{a}(t + \Delta t)] from the interaction potential
>using [image: \vec{x}(t + \Delta t)]
>4. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}\left(t +
>\tfrac12\,\Delta t\right) + \tfrac12\,\vec{a}(t + \Delta t)\Delta t,]
>
>
>
>1. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) + \vec{v}(t)\,
>\Delta t+\tfrac12 \,\vec{a}(t)\,\Delta t^2]
>2. Derive [image: \vec{a}(t + \Delta t)] from the interaction potential
>using [image: \vec{x}(t + \Delta t)]
>3. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}(t) +
>\tfrac12\,\left(\vec{a}(t)+\vec{a}(t + \Delta t)\right)\Delta t\,]
>
>
> This is why my confusion arises.
>
>
> 2014-10-15 14:05 GMT+02:00 Justin Lemkul :
>
> >
> >
> > On 10/15/14 7:30 AM, Mario Fernández Pendás wrote:
> >
> >> Dear all,
> >>
> >> I am still interested in some integrator related issues.
> >>
> >> I understand that the easiest way to implement velocity Verlet was to
> >> split
> >> the updates in two updates. But I don't understad the order of those
> >> updates.
> >> I mean why there are two updates for velocities and then the update for
> >> positions?
> >> My intuitive idea would be to update first one half for velocities,
> then a
> >> full step for positions and, finally, using these new positions the
> second
> >> half for velocities.
> >>
> >
> > Yes, there are two separate half-step updates for velocities. The
> > comments in the md.cpp code are quite verbose if you want to trace
> through.
> >
> > -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!
> >
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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Velocity Verlet integrator
Yes, I understand that. But my question is more about why the two velocity
updates are implemented before the position update and not the other way
round?
From the theoretical point of view I would think more in one of the
following schemes:
1. Calculate: [image: \vec{v}\left(t + \tfrac12\,\Delta t\right) =
\vec{v}(t) + \tfrac12\,\vec{a}(t)\,\Delta t\,]
2. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) +
\vec{v}\left(t + \tfrac12\,\Delta t\right)\, \Delta t\,]
3. Derive [image: \vec{a}(t + \Delta t)] from the interaction potential
using [image: \vec{x}(t + \Delta t)]
4. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}\left(t +
\tfrac12\,\Delta t\right) + \tfrac12\,\vec{a}(t + \Delta t)\Delta t,]
1. Calculate: [image: \vec{x}(t + \Delta t) = \vec{x}(t) + \vec{v}(t)\,
\Delta t+\tfrac12 \,\vec{a}(t)\,\Delta t^2]
2. Derive [image: \vec{a}(t + \Delta t)] from the interaction potential
using [image: \vec{x}(t + \Delta t)]
3. Calculate: [image: \vec{v}(t + \Delta t) = \vec{v}(t) +
\tfrac12\,\left(\vec{a}(t)+\vec{a}(t + \Delta t)\right)\Delta t\,]
This is why my confusion arises.
2014-10-15 14:05 GMT+02:00 Justin Lemkul :
>
>
> On 10/15/14 7:30 AM, Mario Fernández Pendás wrote:
>
>> Dear all,
>>
>> I am still interested in some integrator related issues.
>>
>> I understand that the easiest way to implement velocity Verlet was to
>> split
>> the updates in two updates. But I don't understad the order of those
>> updates.
>> I mean why there are two updates for velocities and then the update for
>> positions?
>> My intuitive idea would be to update first one half for velocities, then a
>> full step for positions and, finally, using these new positions the second
>> half for velocities.
>>
>
> Yes, there are two separate half-step updates for velocities. The
> comments in the md.cpp code are quite verbose if you want to trace through.
>
> -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!
>
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>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Velocity Verlet integrator
On 10/15/14 7:30 AM, Mario Fernández Pendás wrote: Dear all, I am still interested in some integrator related issues. I understand that the easiest way to implement velocity Verlet was to split the updates in two updates. But I don't understad the order of those updates. I mean why there are two updates for velocities and then the update for positions? My intuitive idea would be to update first one half for velocities, then a full step for positions and, finally, using these new positions the second half for velocities. Yes, there are two separate half-step updates for velocities. The comments in the md.cpp code are quite verbose if you want to trace through. -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.
Re: [gmx-users] Velocity Verlet integrator
Dear all, I am still interested in some integrator related issues. I understand that the easiest way to implement velocity Verlet was to split the updates in two updates. But I don't understad the order of those updates. I mean why there are two updates for velocities and then the update for positions? My intuitive idea would be to update first one half for velocities, then a full step for positions and, finally, using these new positions the second half for velocities. Maybe I am missunderstanding something. Thank you very much, Mario Fernández-Pendás 2014-03-23 14:33 GMT+01:00 Michael Shirts : > Putting both velocity Verlet and leapfrog Verlet both in Gromacs turns > out to be non-trivial for the bookkeeping. The easiest way to do this > was split the velocity Verlet updates. > > Also, the additional computational cost of two half steps for > velocities is trivial compared to the cost of the forces for almost > all systems. > > On Sun, Mar 23, 2014 at 8:39 AM, Mario Fernández Pendás > wrote: > > Dear all, > > > > In terms of computational efficiency, why the velocity Verlet integrator > is > > implemented in GROMACS in one full step for positions and two half steps > > for velocities? > > > > Would it be more efficient to merge the second halft step for velocities > > with the first half step of the following scheme, ie, integrating in one > > full step for velocities? > > > > Thank you very much, > > Mario Fernánez-Pendás > > -- > > 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. > -- 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] Velocity Distribution Calculation
On 8/7/14, 7:02 AM, 朱文鹏 wrote: Dear all, I posted it days before. But no one replied. I am wondering if someone has any suggestions about calculation of velocity distribution. Select groups using g_select, extract velocities with g_traj, and create distributions with g_analyze. -Justin Thank you very much. Best, Jason 2014-08-05 23:55 GMT-04:00 : Dear all, I am a new user of GROMACS. Now I am using it on water permeability through a nano-channel. The pressure difference is applied by adding acceleration to water molecules in a periodic simulation box. To get the flow rate of water, I need to the number of water molecules through the channel or spatial velocity distribution in different regions. I used to do similar simulations by LAMMPS. LAMMPS provides the function of "count (region, group)" or the command of "fix ave/spatial" for counting atom number or velocity distribution. I am wondering how I can do it in GROMACS. Does it have the same commands? I went over the manual and saw commands of "g_traj" and "g_spatial". Are they what I am looking for? Thank you very much for your attention. Best, Jason -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] Velocity Distribution Calculation
Dear all, I posted it days before. But no one replied. I am wondering if someone has any suggestions about calculation of velocity distribution. Thank you very much. Best, Jason 2014-08-05 23:55 GMT-04:00 : > Dear all, > > I am a new user of GROMACS. Now I am using it on water permeability > through a nano-channel. The pressure difference is applied by adding > acceleration to water molecules in a periodic simulation box. To get the > flow rate of water, I need to the number of water molecules through the > channel or spatial velocity distribution in different regions. > > I used to do similar simulations by LAMMPS. LAMMPS provides the function > of "count (region, group)" or the command of "fix ave/spatial" for counting > atom number or velocity distribution. I am wondering how I can do it in > GROMACS. Does it have the same commands? I went over the manual and saw > commands of "g_traj" and "g_spatial". Are they what I am looking for? > > Thank you very much for your attention. > > Best, > Jason > -- 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] Velocity Distribution Calculation
Dear all, I am a new user of GROMACS. Now I am using it on water permeability through a nano-channel. The pressure difference is applied by adding acceleration to water molecules in a periodic simulation box. To get the flow rate of water, I need to the number of water molecules through the channel or spatial velocity distribution in different regions. I used to do similar simulations by LAMMPS. LAMMPS provides the function of "count (region, group)" or the command of "fix ave/spatial" for counting atom number or velocity distribution. I am wondering how I can do it in GROMACS. Does it have the same commands? I went over the manual and saw commands of "g_traj" and "g_spatial". Are they what I am looking for? Thank you very much for your attention. Best, Jason -- 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] Velocity Verlet integrator
Putting both velocity Verlet and leapfrog Verlet both in Gromacs turns out to be non-trivial for the bookkeeping. The easiest way to do this was split the velocity Verlet updates. Also, the additional computational cost of two half steps for velocities is trivial compared to the cost of the forces for almost all systems. On Sun, Mar 23, 2014 at 8:39 AM, Mario Fernández Pendás wrote: > Dear all, > > In terms of computational efficiency, why the velocity Verlet integrator is > implemented in GROMACS in one full step for positions and two half steps > for velocities? > > Would it be more efficient to merge the second halft step for velocities > with the first half step of the following scheme, ie, integrating in one > full step for velocities? > > Thank you very much, > Mario Fernánez-Pendás > -- > 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.
[gmx-users] Velocity Verlet integrator
Dear all, In terms of computational efficiency, why the velocity Verlet integrator is implemented in GROMACS in one full step for positions and two half steps for velocities? Would it be more efficient to merge the second halft step for velocities with the first half step of the following scheme, ie, integrating in one full step for velocities? Thank you very much, Mario Fernánez-Pendás -- 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] velocity generation
On 12/5/13 12:36 PM, kiana moghaddam wrote: Dear GMX user I want to use NVT to heat my system (DNA-ligand) from 0 to 300K then NPT at 300 K in equilibration step. I 'm very confused about velocity generation. I use gen_vel= no in the first step (NVT) then generate velocity in the NPT step at 300 K. After that, in production step I use gen_vel= no. Is my process correct? If you generate new velocities at the outset of NPT, it introduces new instability and basically negates any benefit of having done any prior equilibration. Preserve the velocities from NVT (via the .cpt file) when continuing to NPT. Rule of thumb: do not generate velocities for any step in the protocol that is not the very first one. There are exceptions, but they are generally rare. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] velocity generation
On 12/5/13 1:21 PM, kiana moghaddam wrote: Dear Jastin Thanks your reply. as your email, I will generate velocity in NVT step with simulated annealing from 0 to 300K. What should be gen_temp value? Is 300 K correct? This topic has been discussed repeatedly in the last few days. Please see the previous responses. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] velocity generation
Dear Jastin Thanks your reply. as your email, I will generate velocity in NVT step with simulated annealing from 0 to 300K. What should be gen_temp value? Is 300 K correct? Best Regards On Thursday, December 5, 2013 9:15 PM, Justin Lemkul wrote: On 12/5/13 12:36 PM, kiana moghaddam wrote: > Dear GMX user > > I want to use NVT to heat my system (DNA-ligand) from 0 to 300K then NPT at > 300 K in equilibration step. > I 'm very confused about velocity generation. > I use gen_vel= no in the first step (NVT) then generate velocity in the NPT > step at 300 K. After that, in production step I use gen_vel= no. Is my > process correct? > If you generate new velocities at the outset of NPT, it introduces new instability and basically negates any benefit of having done any prior equilibration. Preserve the velocities from NVT (via the .cpt file) when continuing to NPT. Rule of thumb: do not generate velocities for any step in the protocol that is not the very first one. There are exceptions, but they are generally rare. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] velocity generation
Dear GMX user I want to use NVT to heat my system (DNA-ligand) from 0 to 300K then NPT at 300 K in equilibration step. I 'm very confused about velocity generation. I use gen_vel= no in the first step (NVT) then generate velocity in the NPT step at 300 K. After that, in production step I use gen_vel= no. Is my process correct? Thank you Best Regards -- 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.
