[gmx-users] PMF - US histograms problem
Hi everyone, I'm trying to calculate the PMF for the extraction of a peptide from within a peptide nanostructure. However I'm having difficulty to overlap the histograms for the first pulling windows: Many full overlap windows follow by a large gap with no histogram. I've tried the two things I could: reduce the distance increment between the windows (now I'm using 0.05nm), and I've already done several tests with different force constants with k up to 2! For each window test I run only 1ns of sampling. Anyone have any suggestions? Could another umbrella sampling scheme (constraint pulling) be more efficient in this case? Bests ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Av. Cesar Lattes, 1201, Eugênio de Mello, SP, 12247-014 -- 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] HB analysis at surfaces
Hello Zarrini, thank you very much for the answer. Unfortunately g_density is not the right tool. With it for example it is not possible to visualize the characteristic peaks of the formation of the hydrogen bond in the distribution O ... H. This is because g_density does not parse pairs but rather the amount of atoms in a slice of the box. Figure 5 from this paper 10.1021/la803324x shows the analysis that I would like to do. If I'm not mistaken, the authors used a hacked g_rdf tool to construct it. I even tried to contact them directly but I got no response. Bests eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Av. Cesar Lattes, 1201, Eugênio de Mello, SP, 12247-014 > > -- > > Message: 5 > Date: Fri, 27 Jan 2017 20:19:25 +0100 > From: Salman Zarrini <salman.zarr...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] HB analysis at surfaces > Message-ID: > <CAD6yk5DQ6LgHBysfAOMcBfE7RxfPRwouEp1TGhOMQLMgN34JwA@mail. > gmail.com> > Content-Type: text/plain; charset=UTF-8 > > If you mean water profile density then "gmx density" is your friend. Just > invoke below command and play around with the variables to reach your > desire. > > gmx density -f case.trr -s case.tpr -n index.ndx -d Z -dens mass -o WD.xvg > -b 10000 -sl 5000 > > > Cheers, > > S.Zarrini > > > On Fri, Jan 27, 2017 at 5:18 PM, Eudes Fileti <fil...@gmail.com> wrote: > > > Hello everyone, > > I'm interested in calculating distributions of O...H pairs between water > > and a hydrophilic surface. For this I need a tool that allows the > > calculation of a "g(z)" (that is, a rdf that is not radial, but rather > > depends only on the distance z to the surface). > > > > Anyone have this tool ready? If not, can anyone suggest me how and which > > gmx tool I could change to achieve this? > > > > Bests > > > > ___ > > Eudes Eterno Fileti > > Instituto de Ci?ncia e Tecnologia da UNIFESP > > Av. Cesar Lattes, 1201, Eug?nio de Mello, SP, 12247-014 > > -- > -- 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] HB analysis at surfaces
Hello everyone, I'm interested in calculating distributions of O...H pairs between water and a hydrophilic surface. For this I need a tool that allows the calculation of a "g(z)" (that is, a rdf that is not radial, but rather depends only on the distance z to the surface). Anyone have this tool ready? If not, can anyone suggest me how and which gmx tool I could change to achieve this? Bests ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Av. Cesar Lattes, 1201, Eugênio de Mello, SP, 12247-014 -- 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] Gromacs in Mac OS 10.11 (el capitan) (Eudes Fileti) (SOLVED)
Hello gmx-users, I managed to install the gromacs 5.1.2 in El capitan simply deleting the option "-DREGRESSIONTEST_DOWNLOAD=ON" from cmake command. So, the script I used for dirty installation was: cd gromacs-5.1.2 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC bests eef -- > > Message: 4 > Date: Fri, 3 Jun 2016 17:36:17 -0300 > From: Eudes Fileti <fil...@gmail.com> > To: gmx-us...@gromacs.org > Subject: [gmx-users] Gromacs in Mac OS 10.11 (el capitan) > Message-ID: >
[gmx-users] Gromacs in Mac OS 10.11 (el capitan)
Hi, I'm following the standard script below for Gromacs installation, as usual I do: mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install But this time I'm getting a strange error after "cmake" command: fileti:~/Downloads/gromacs-5.1.2/build$make [ 1%] Built target fftwBuild make[2]: *** No rule to make target `/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/System/Library/Frameworks/Accelerate.framework', needed by `lib/libgromacs.1.2.0.dylib'. Stop. make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 make: *** [all] Error 2 Someone also had any problems withMac OS 10.11 (el capitan) to INSTALLING gromacs? Any suggestion? Bests eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Av. Cesar Lattes, 1201, Eugênio de Mello, SP, 12247-014 -- 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] PMF using umbrella sampling and Gromacs 5.0
Dear Chris, thanks for the help. Yes, I set the temperature properly. Also I checked the line that you mentioned and it is exactly the same in my version of gromacs (5.0.4). I have not yet tried using another tool wham. I'll search the web and if I find something, I report shortly. eef Dear Eudes: then I return to being stumped. It sure looks like it might be an issue with a constant somewhere. I'll note that v5.0.5 g_wham uses what I think is an incorrect constant to convert to kcal (http://redmine.gromacs.org/issues/1787), but you're using kj so that shouldn't be it. The gas constant defined by g_wham on line 1086 in v5.0.5 is also a little bit different from the one used in core gromacs (for e.g. replica exchange to get the boltzmann constant), though again I don't see how this could do anything but affect the overall scale by a tiny amount. However, I do wonder about 8.314e-3 in lines like this where it possibly could affect the value: denom += invg*window[j].N[k]*exp(-U/(8.314e-3*opt-Temperature) + window[j].z[k]); (line 966 in calc_profile() in v5.0.5) Are you using g_wham? Can you try a different wham software and see if you get the same thing? Also, are you setting -temp properly in g_wham ? Beyond that, I've run out of ideas. If you do ever sort this out, I'd appreciate it if you could send me an email off list to let me know (and post it here of course, I just don't always check the list). Thank you, Chris. ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Página: sites.google.com/site/fileti/ On 28 July 2015 at 08:59, Eudes Fileti fil...@gmail.com wrote: Dear Chris, thank you for help. I performed the test you suggested, with no pressure coupling. Note that the behavior of the profile remained the same even with no pressure coupling. https://goo.gl/photos/2d8tsYFwp2eHCuCWA The simulation parameters were exactly the same (except the sampling in the test was 5 ns window and by coupling pressure, which was turned off). Bests eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Página: sites.google.com/site/fileti/ -- Message: 2 Date: Sun, 26 Jul 2015 02:45:50 + From: Christopher Neale chris.ne...@alum.utoronto.ca To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti) Message-ID: blupr03mb184037e6ef2ec6d63bebe21c5...@blupr03mb184.namprd03.prod.outlook.com Content-Type: text/plain; charset=iso-8859-1 Dear Eudes: Glad that you solved one of the two issues. As for the bumps in the PMF, I have a new theory: the bumps come from pressure coupling. When the sampled distance, d, between the two molecules fluctuate a little closer than the center of restraint, d0, that adds a repulsive force that contributes to the virial and the box gets a little larger. Conversely, slight fluctuations of d that are larger than d0 will add a small bias to box contraction. This should be more noticeable when the restrained distance involves larger masses. It is at the moment unclear to me whether this might exert an effect indirectly due to overall system density or more directly as coordinate scaling impacts the instantaneous value of d. If it is the latter, then semi-isotropic pressure coupling, may also enhance the effect since the virial will be computed independently along the order parameter (I presume) and hence there is less noise from other dimensions. Can you please try again without pressure coupling (single precision should be fine for this test). Hopefully this is not the source of the bumps because, if it is affecting the PMF noticeably and the underlying free energy surface has a large gradient, then d will always be on one side of d0 and the effect will not be merely bumps but also some type of bias in the PMF. Whether this bias is accurate or artifactual falls outside of my mathematical abilities. The thing is, the force is a real force between real atoms so it seems like it really should be included in the virial (as it certainly is... I checked). I can tell you one thing for sure: the effect on box volume is real and noticeable. That is, if you look at the average system volume when dd0, it differs in a statistically significant manner from the average system volume when dd0 (something that I also checked). Thank you for looking into this further, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eudes Fileti fil...@gmail.com Sent: 24 July 2015 16:47 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes
Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0
Dear Chris, thank you for help. I performed the test you suggested, with no pressure coupling. Note that the behavior of the profile remained the same even with no pressure coupling. https://goo.gl/photos/2d8tsYFwp2eHCuCWA The simulation parameters were exactly the same (except the sampling in the test was 5 ns window and by coupling pressure, which was turned off). Bests eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Página: sites.google.com/site/fileti/ -- Message: 2 Date: Sun, 26 Jul 2015 02:45:50 + From: Christopher Neale chris.ne...@alum.utoronto.ca To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti) Message-ID: blupr03mb184037e6ef2ec6d63bebe21c5...@blupr03mb184.namprd03.prod.outlook.com Content-Type: text/plain; charset=iso-8859-1 Dear Eudes: Glad that you solved one of the two issues. As for the bumps in the PMF, I have a new theory: the bumps come from pressure coupling. When the sampled distance, d, between the two molecules fluctuate a little closer than the center of restraint, d0, that adds a repulsive force that contributes to the virial and the box gets a little larger. Conversely, slight fluctuations of d that are larger than d0 will add a small bias to box contraction. This should be more noticeable when the restrained distance involves larger masses. It is at the moment unclear to me whether this might exert an effect indirectly due to overall system density or more directly as coordinate scaling impacts the instantaneous value of d. If it is the latter, then semi-isotropic pressure coupling, may also enhance the effect since the virial will be computed independently along the order parameter (I presume) and hence there is less noise from other dimensions. Can you please try again without pressure coupling (single precision should be fine for this test). Hopefully this is not the source of the bumps because, if it is affecting the PMF noticeably and the underlying free energy surface has a large gradient, then d will always be on one side of d0 and the effect will not be merely bumps but also some type of bias in the PMF. Whether this bias is accurate or artifactual falls outside of my mathematical abilities. The thing is, the force is a real force between real atoms so it seems like it really should be included in the virial (as it certainly is... I checked). I can tell you one thing for sure: the effect on box volume is real and noticeable. That is, if you look at the average system volume when dd0, it differs in a statistically significant manner from the average system volume when dd0 (something that I also checked). Thank you for looking into this further, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eudes Fileti fil...@gmail.com Sent: 24 July 2015 16:47 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti) Hello Chris, I write to report the results of the tests you suggested. To recap, I have two problems to solve. 1) The bad sampling around z = 0 and 2) the bumps along to the profile. I solved the first discarding all the my initial configurations and performing a new pulling (SMD). Only this time I used a higher force constant (5000 kJ/mol nm2). Thus I got configurations close to z = 0, where they were not generated. For the second problem, you suggested recalculate the PMF using double precision. The results of this test showed that it does not solve the problem, on the contrary the bumps were even more pronounced, as indicated by the plot in this link. https://goo.gl/photos/wGNhdyNG9pdqGfcB6 All tests were performed with prototypes simulations, with 40 windows of 2 ns spaced by 0.1 nm. A larger sample is obviously necessary for reliable profiles, but this was enough to show the trend that I wanted to watch. As I have mentioned before, I've done several tests aiming to eliminate these bumps: use of higher sampling, up to 20ns per window; reducing the spacing between the windows (from 0.1 to 0.05 nm); changing the spring constant from 1000 up to 5000 kJ/mol nm2, use of two different versions of the Gromacs (4.6 e 5.0) and also I tested it with two different sets of initial settings. None of this attempts solved the bumps problem. If you (or someone else) have any other tips please let me know. Thank you eef ___ Eudes Eterno Fileti Instituto de Ci?ncia e Tecnologia da UNIFESP Rua Talim, 330, S?o Jos? dos Campos - SP P?gina: sites.google.com/site/fileti/ -- Message: 4 Date: Wed, 22
Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0
Dear Chris, thank you for help. I performed the test you suggested, with no pressure coupling. Note that the behavior of the profile remained the same even with no pressure coupling. https://goo.gl/photos/2d8tsYFwp2eHCuCWA The simulation parameters were exactly the same (except the sampling in the test was 5 ns window and by coupling pressure, which was turned off). Bests eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Página: sites.google.com/site/fileti/ -- Message: 2 Date: Sun, 26 Jul 2015 02:45:50 + From: Christopher Neale chris.ne...@alum.utoronto.ca To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti) Message-ID: blupr03mb184037e6ef2ec6d63bebe21c5...@blupr03mb184.namprd03.prod.outlook.com Content-Type: text/plain; charset=iso-8859-1 Dear Eudes: Glad that you solved one of the two issues. As for the bumps in the PMF, I have a new theory: the bumps come from pressure coupling. When the sampled distance, d, between the two molecules fluctuate a little closer than the center of restraint, d0, that adds a repulsive force that contributes to the virial and the box gets a little larger. Conversely, slight fluctuations of d that are larger than d0 will add a small bias to box contraction. This should be more noticeable when the restrained distance involves larger masses. It is at the moment unclear to me whether this might exert an effect indirectly due to overall system density or more directly as coordinate scaling impacts the instantaneous value of d. If it is the latter, then semi-isotropic pressure coupling, may also enhance the effect since the virial will be computed independently along the order parameter (I presume) and hence there is less noise from other dimensions. Can you please try again without pressure coupling (single precision should be fine for this test). Hopefully this is not the source of the bumps because, if it is affecting the PMF noticeably and the underlying free energy surface has a large gradient, then d will always be on one side of d0 and the effect will not be merely bumps but also some type of bias in the PMF. Whether this bias is accurate or artifactual falls outside of my mathematical abilities. The thing is, the force is a real force between real atoms so it seems like it really should be included in the virial (as it certainly is... I checked). I can tell you one thing for sure: the effect on box volume is real and noticeable. That is, if you look at the average system volume when dd0, it differs in a statistically significant manner from the average system volume when dd0 (something that I also checked). Thank you for looking into this further, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eudes Fileti fil...@gmail.com Sent: 24 July 2015 16:47 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti) Hello Chris, I write to report the results of the tests you suggested. To recap, I have two problems to solve. 1) The bad sampling around z = 0 and 2) the bumps along to the profile. I solved the first discarding all the my initial configurations and performing a new pulling (SMD). Only this time I used a higher force constant (5000 kJ/mol nm2). Thus I got configurations close to z = 0, where they were not generated. For the second problem, you suggested recalculate the PMF using double precision. The results of this test showed that it does not solve the problem, on the contrary the bumps were even more pronounced, as indicated by the plot in this link. https://goo.gl/photos/wGNhdyNG9pdqGfcB6 All tests were performed with prototypes simulations, with 40 windows of 2 ns spaced by 0.1 nm. A larger sample is obviously necessary for reliable profiles, but this was enough to show the trend that I wanted to watch. As I have mentioned before, I've done several tests aiming to eliminate these bumps: use of higher sampling, up to 20ns per window; reducing the spacing between the windows (from 0.1 to 0.05 nm); changing the spring constant from 1000 up to 5000 kJ/mol nm2, use of two different versions of the Gromacs (4.6 e 5.0) and also I tested it with two different sets of initial settings. None of this attempts solved the bumps problem. If you (or someone else) have any other tips please let me know. Thank you eef ___ Eudes Eterno Fileti Instituto de Ci?ncia e Tecnologia da UNIFESP Rua Talim, 330, S?o Jos? dos Campos - SP P?gina: sites.google.com/site/fileti/ -- Message: 4 Date: Wed, 22
Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti)
of the center of mass position of the membrane, the minimum distance is never zero, as shown in the graphs of my pulling below. What is the effect of this difference in the calculation of the PMF? Could this be the source of my problem? https://goo.gl/photos/cwwLzog6wXAgVJG88 Bests eef PS. I found this paper below where authors have published this unusual behavior (Figure 4). They did not explain the reason for the oscillations at large distances and I also do not know why this occurs. http://www.mdpi.com/1422-0067/13/11/14451/htm From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eudes Fileti fil...@gmail.com Sent: 18 July 2015 21:06 To: gmx-us...@gromacs.org Subject: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 Hello guys, I'm trying to calculate the PMF using umbrella sampling for a small molecule to penetrate a lipid membrane. The 1D reaction coordinate is along the z axis, which corresponds to the bilayer normal. The umbrella potential acts on the center of mass of the molecule. The initial configurations for each window, separated by a distance of 0.1nm, in a range of 4 nm (distance between the centers of mass of the membrane and the molecule), were obtained by a SMD. The umbrella potential was applied according to the parameters below (for Gromacs version 5.0.3). Each window was sampled by 5 ns. ; COM PULLING pull = umbrella pull_geometry= direction pull_dim = N N Y pull_start = yes pull-print-reference = no pull_nstxout = 1000 pull_nstfout = 1000 pull_ngroups = 2 pull-ncoords = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull-group1-name = DPPC ; ref pull-group2-name = LIG ; pulled pull-coord1-groups = 1 2 pull-coord1-origin = 0 0 0 pull-coord1-vec = 0 0 1 pull-coord1-init = 0 pull-coord1-rate = 0.0 pull-coord1-k= 3000 Histograms and the PMF obtained are shown in figure the link below. https://goo.gl/photos/RkW9gbWrgeKEfV3R7 I repeated the same test using other parameters (larger and small k values) and options (cylinder and position, for this later I have used gmx 4.6) and so far I could not get a satisfactory profile. In all tests, a problem that I have observed is that the region near z = 0 is not sampled (there is a gap between 0.0 and 0.5 nm). In addition the profile presents not smooth, but somehow oscillating mainly for large z. As the gmx distance give a value different of zero for the smallest distance of separation between the centers of mass (around 0.1-0.2 nm) I believe that this weird behavior is related to the reference distance that I have used. Could someone give me a light? Most of the tips I read in GMX list are related to previous versions of the Gromacs and in a way the other tips were already included in my tests. Thank you eef ___ Eudes Eterno Fileti Instituto de Ci?ncia e Tecnologia da UNIFESP Rua Talim, 330, S?o Jos? dos Campos - SP P?gina: sites.google.com/site/fileti/ -- 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] PMF using umbrella sampling and Gromacs 5.0
Hello guys, I'm trying to calculate the PMF using umbrella sampling for a small molecule to penetrate a lipid membrane. The 1D reaction coordinate is along the z axis, which corresponds to the bilayer normal. The umbrella potential acts on the center of mass of the molecule. The initial configurations for each window, separated by a distance of 0.1nm, in a range of 4 nm (distance between the centers of mass of the membrane and the molecule), were obtained by a SMD. The umbrella potential was applied according to the parameters below (for Gromacs version 5.0.3). Each window was sampled by 5 ns. ; COM PULLING pull = umbrella pull_geometry= direction pull_dim = N N Y pull_start = yes pull-print-reference = no pull_nstxout = 1000 pull_nstfout = 1000 pull_ngroups = 2 pull-ncoords = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull-group1-name = DPPC ; ref pull-group2-name = LIG ; pulled pull-coord1-groups = 1 2 pull-coord1-origin = 0 0 0 pull-coord1-vec = 0 0 1 pull-coord1-init = 0 pull-coord1-rate = 0.0 pull-coord1-k= 3000 Histograms and the PMF obtained are shown in figure the link below. https://goo.gl/photos/RkW9gbWrgeKEfV3R7 I repeated the same test using other parameters (larger and small k values) and options (cylinder and position, for this later I have used gmx 4.6) and so far I could not get a satisfactory profile. In all tests, a problem that I have observed is that the region near z = 0 is not sampled (there is a gap between 0.0 and 0.5 nm). In addition the profile presents not smooth, but somehow oscillating mainly for large z. As the gmx distance give a value different of zero for the smallest distance of separation between the centers of mass (around 0.1-0.2 nm) I believe that this weird behavior is related to the reference distance that I have used. Could someone give me a light? Most of the tips I read in GMX list are related to previous versions of the Gromacs and in a way the other tips were already included in my tests. Thank you eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Página: sites.google.com/site/fileti/ -- 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] Vacuum simulation in GMX 5
Justin, thanks for the help. Originally I have tried the options you suggested, and the GMX 5 not accepted well, since there are not more -pd option, which allowed to perform the calculation with pbc = no. So, you asked me to see my input. The first test I did was obviously considering cut-offs, since I needed impose pbc = yes. These parameters are the ones I sent you. Of course plain cutoffs is not dealing well with the electrostatic part, but in this case I was only doing just a quick test. You said you have made calculations for a molecule of 50 atoms at a rate of 130ns/day on a single core. Did you used to that Gromacs 5? What are the mdp options that you use in this case? eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Página: sites.google.com/site/fileti/ -- 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] Vacuum simulation in GMX 5 (Justin Lemkul)
Hi Justin, this is my mdp options. thanks eef ; Run control define = -DPOSRES integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 500; 100 ps nstcomm = 100 ; Output control nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 100 nstenergy= 100 nstxout-compressed = 0 ; Neighborsearching and short-range nonbonded interactions cutoff-scheme= verlet nstlist = 20 ns_type = grid pbc = xyz rlist= 1.2 ; Electrostatics coulombtype = cut-off rcoulomb = 1.2 ; van der Waals vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no ; Groups to couple separately tc-grps = system ; Time constant (ps) and reference temperature (K) tau-t= 0.1 ref-t= 323 ; pressure coupling Pcoupl = no Pcoupltype = isotropic nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 2.0 compressibility = 4.5e-5 ref-p= 1.0 ; Scaling of reference coordinates, No, All or COM refcoord-scaling = com ; Free energy control stuff free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1; only immediate neighboring windows vdw_lambdas = 0.00 0.00 0.00 0... .70 0.75 0.80 0.85 0.90 0.95 1.00 coul_lambdas = 0.00 0.05 0.10 01.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ; Options for the decoupling sc-alpha = 0.5 sc-coul = no ; linear interpolation of Coulomb (none in this case) sc-power = 1.0 sc-sigma = 0.3 couple-moltype = Pept ; name of moleculet ype to decouple couple-lambda0 = vdw-q ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW couple-intramol = yes nstdhdl = 10 ; Generate velocities to start gen_vel = yes gen_temp = 300 gen_seed = -1 ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Do not constrain the starting configuration continuation = no ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Página: sites.google.com/site/fileti/ On 6 May 2015 at 14:04, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: Constraint of active site in gromacs (Mark Abraham) 2. Re: Constraint of active site in gromacs (Nataraj Balakrishnan) 3. on a MD run notice (Brett) 4. Re: on a MD run notice (Justin Lemkul) 5. Vacuum simulation in GMX 5 (Eudes Fileti) 6. Re: Vacuum simulation in GMX 5 (Justin Lemkul) -- -- Message: 5 Date: Wed, 6 May 2015 13:54:28 -0300 From: Eudes Fileti fil...@gmail.com To: gmx-us...@gromacs.org Subject: [gmx-users] Vacuum simulation in GMX 5 Message-ID: CAHC5Q= gbdfnhmxhnzcpditqelxmsfpqig9uf-ck3c+rjsck...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hello, in the previous gmx versions I could accelerate simulations in vacuum making the cutting cut-offs zero
[gmx-users] Vacuum simulation in GMX 5
Hello, in the previous gmx versions I could accelerate simulations in vacuum making the cutting cut-offs zero and pbc = no. However, now it is no longer current possible with GMX 5 (since pbc = no is not supported with dd, and the particle decomposition mode is not suported in GMX 5). Does anyone have any tips to speed up a calculation in vacuum? I'm decoupling a small molecule in vacuum (for an free energy calculation) at a rate of 1ns/h, which seems very slow. eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Página: sites.google.com/site/fileti/ -- 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] gromacs.org_gmx-users Digest, Vol 133, Issue 30
Hi Justin, this is my mdp options. thanks eef ; Run control define = -DPOSRES integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 500; 100 ps nstcomm = 100 ; Output control nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 100 nstenergy= 100 nstxout-compressed = 0 ; Neighborsearching and short-range nonbonded interactions cutoff-scheme= verlet nstlist = 20 ns_type = grid pbc = xyz rlist= 1.2 ; Electrostatics coulombtype = cut-off rcoulomb = 1.2 ; van der Waals vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no ; Groups to couple separately tc-grps = system ; Time constant (ps) and reference temperature (K) tau-t= 0.1 ref-t= 323 ; pressure coupling Pcoupl = no Pcoupltype = isotropic nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 2.0 compressibility = 4.5e-5 ref-p= 1.0 ; Scaling of reference coordinates, No, All or COM refcoord-scaling = com ; Free energy control stuff free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1; only immediate neighboring windows vdw_lambdas = 0.00 0.00 0.00 0... .70 0.75 0.80 0.85 0.90 0.95 1.00 coul_lambdas = 0.00 0.05 0.10 01.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ; Options for the decoupling sc-alpha = 0.5 sc-coul = no ; linear interpolation of Coulomb (none in this case) sc-power = 1.0 sc-sigma = 0.3 couple-moltype = Pept ; name of moleculet ype to decouple couple-lambda0 = vdw-q ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW couple-intramol = yes nstdhdl = 10 ; Generate velocities to start gen_vel = yes gen_temp = 300 gen_seed = -1 ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Do not constrain the starting configuration continuation = no ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Página: sites.google.com/site/fileti/ On 6 May 2015 at 14:04, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: Constraint of active site in gromacs (Mark Abraham) 2. Re: Constraint of active site in gromacs (Nataraj Balakrishnan) 3. on a MD run notice (Brett) 4. Re: on a MD run notice (Justin Lemkul) 5. Vacuum simulation in GMX 5 (Eudes Fileti) 6. Re: Vacuum simulation in GMX 5 (Justin Lemkul) -- Message: 1 Date: Wed, 06 May 2015 14:37:38 + From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Constraint of active site in gromacs Message-ID: camnumarhm6ieyijutegdosf2ok7qekkcxbktfom43ynj02r...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Yes, but you need distance restraints (not constraints, which are different) like Justin said. You also need to get both
