[gmx-users] DSSP
Dear all, How do i install DSSP for gromacs 5.1.1 I am curently working on Centos Which version should i download and any commands to install dssp Thanks & Regards Sanket -- 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] Fw: lipid pulling
Dear all, I am pulling the saturated and unsaturated chains of a lipid bilayer to "simulate" its gel phase transition by pull code. It ends with the expected extended structure. But when I continue with zero pulling rate to maintain the extended structure for a while, the tails go back to the original length. I guess I have made some mistakes in the mdp pull code part, = pull= umbrella pull-ngroups= 6 pull-ncoords= 4 pull-group1-name= topC2 pull-group2-name= downC2 pull-group3-name= topC218 pull-group4-name= downC218 pull-group5-name= topC316 pull-group6-name= downC316 pull-geometry= distance ; simple distance increase pull-coord1-groups = 1 3 pull-coord2-groups = 1 5 pull-coord3-groups = 2 4 pull-coord4-groups = 2 6 pull-dim = N N Y pull-coord1-vec = 0 0 1 pull-coord1-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns pull-coord1-k = 1000 ; kJ mol^-1 nm^-2 pull-coord2-vec = 0 0 1 pull-coord2-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns pull-coord2-k = 1000 ; kJ mol^-1 nm^-2 pull-coord3-vec = 0 0 1 pull-coord3-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns pull-coord3-k = 1000 ; kJ mol^-1 nm^-2 pull-coord4-vec = 0 0 1 pull-coord4-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns pull-coord4-k = 1000 ; kJ mol^-1 nm^-2 pull-coord1-init= 1.0 pull-coord2-init= 1.0 pull-coord3-init= 1.0 pull-coord4-init= 1.0 pull-start = yes ; define initial COM distance > 0 Any guess on the reason? Many thanks. Best, Yao -- -- 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] Copernicus
Hi all, There is a tool called Copernicus (http://copernicus-computing.org/about/) for automating Gromacs simulations. Has anybody here used it and can maybe help me out a bit? Specifically, I'm interested in how to get multiple servers working in a network and sharing a workload. Apologies for not directly Gromacs-related question but since Copernicus seems to be used solely for Gromacs simulations I hope I can get away with it.. Regards, Kalev -- 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] mdrun rerun to large frame numbers
Hey, I try to perform an rerun of very long trajectories using mdrun. The problem is, that the rerun crashes after it reaches a certain frame number with the warning: there may be something wrong with the energy file XXX.edr Found: step=-1983077269, nre=49, nblock=0, time=4.62378e+06. Trying to skip frame expect a crash though. I tried it for three different runs and I get always the same warning. The step number is something strange. Best, Basti -- 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] DSSP
Hi, gmx do_dssp -h has some useful instructions. Mark On Thu, Jul 7, 2016 at 9:04 AM Sanket Ghawali wrote: > Dear all, > How do i install DSSP for gromacs 5.1.1 > I am curently working on Centos > Which version should i download and any commands to install dssp > > Thanks & Regards > Sanket > -- > 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] mdrun rerun to large frame numbers
Hi, Hmm, that sounds like your very long trajectory is running into some integer exceeding its maximum size. mdrun proper uses a 64-bit integer for step number, but doubtless there are dusty corners. Are you able to estimate which frame number this was? What does gmx check say about the very long trajectory? To work around it, you can probably just use gmx trjconv to break the trajectory into parts, but we'd rather find the problem and fix it :-) Mark On Thu, Jul 7, 2016 at 11:59 AM Sebastian < sebastian.buchenb...@physik.uni-freiburg.de> wrote: > Hey, > > I try to perform an rerun of very long trajectories using mdrun. > The problem is, that the rerun crashes after it reaches a certain frame > number with the warning: > > there may be something wrong with the energy file XXX.edr > Found: step=-1983077269, nre=49, nblock=0, time=4.62378e+06. > Trying to skip frame expect a crash though. > > I tried it for three different runs and I get always the same warning. > The step number is something strange. > > Best, > > Basti > -- > 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] lipid pulling Probelm
Dear all, I am pulling the saturated and unsaturated chains of a lipid bilayer to "simulate" its gel phase transition by pull code. It ends with the expected extended structure. But when I continue with zero pulling rate to maintain the extended structure for a while, the tails go back to the original length. I guess I have made some mistakes in the mdp pull code part, = pull= umbrella pull-ngroups= 6 pull-ncoords= 4 pull-group1-name= topC2 pull-group2-name= downC2 pull-group3-name= topC218 pull-group4-name= downC218 pull-group5-name= topC316 pull-group6-name= downC316 pull-geometry= distance ; simple distance increase pull-coord1-groups = 1 3 pull-coord2-groups = 1 5 pull-coord3-groups = 2 4 pull-coord4-groups = 2 6 pull-dim = N N Y pull-coord1-vec = 0 0 1 pull-coord1-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns pull-coord1-k = 1000 ; kJ mol^-1 nm^-2 pull-coord2-vec = 0 0 1 pull-coord2-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns pull-coord2-k = 1000 ; kJ mol^-1 nm^-2 pull-coord3-vec = 0 0 1 pull-coord3-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns pull-coord3-k = 1000 ; kJ mol^-1 nm^-2 pull-coord4-vec = 0 0 1 pull-coord4-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns pull-coord4-k = 1000 ; kJ mol^-1 nm^-2 pull-coord1-init= 1.0 pull-coord2-init= 1.0 pull-coord3-init= 1.0 pull-coord4-init= 1.0 pull-start = yes ; define initial COM distance > 0 Any guess on the reason? Many thanks. Best, Yao -- -- 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] Calculation of non bonded interaction
Hi, I want to calculate non bonded interaction between an ion pair (say "A" and "B"). There are total 125 ion pairs in the system. How could I calculate the average non bonded interaction between one cation and anion in the system? Thanks, Pravin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GMX Density – Setting Start and End Position Along Z Axis
On 7/5/16 1:18 PM, ALEXANDER DHALIWAL wrote: Hi Justin, Thank you for such a prompt reply. I am currently using the -center option in my density calculation; an example of my code is: gmx density -f md_1_5_cat.trr -s md_1_5_cat.tpr -ei electrons.dat -n popc_densities.ndx -o test.xvg -center ... Select the group to center density profiles around: Group 2 (POPC) Select 1 group to calculate density for: Group 5 (SOL) However, the output when run for two different system generates equally spaced intervals that don't necessarily line up. So, when I want to evaluate the difference at, say, the peak of the electron density map, the z-values between my two maps do not correspond. I believe that if I could specify the number of slices using the -sl designation and specify the bounds that I need for the density calculations, each of my .xvg density files would have the same z-coordinates between them, and their differences could be directly evaluated. Is this possible? No combination of using -center, -symm, and -relative so far has helped me achieve this yet. Can you provide an image that illustrates your problem? I can't visualize how the problem is arising. If the bilayer is the same, centering on it should remove any issue associated with different box sizes; the position relative to the center should be similar. Maybe I'm just missing something here that is specific to the setup of your system. Additionally, I am currently using the following link to inform me on different gromacs functions. Is it possible to receive more information on these functions besides sifting through archived emails? http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/onlinehelp/gmx-density.html Help info can be printed directly by every tool, e.g. gmx help density or gmx density -h. -Justin Thanks again! – Alex On Tue, Jul 5, 2016 at 12:55 PM, Justin Lemkul wrote: On 7/5/16 10:27 AM, ALEXANDER DHALIWAL wrote: Hello: I am attempting to use the gmx density function to calculate the electron density of a bilayer system with and without a solute. In order to do this, I must calculate the density of various elements (i.e., lipid head groups, lipid tails, solvent molecules) along the bilayer normal (z axis) for both a pure bilayer system that I have run and a similar one containing the solute, and then I must find the difference between the respective electron density profiles. However, each system has slightly different box z-dimensions, so the two instances of running the gmx density command result in differently spaced intervals along the axis. This makes it hard to compute the difference. Is there a specification by which I can choose the starting and ending place along the z-axis for my density calculation, such that I can have even intervals spaced at the same places for both of my calculations? I have tried changing the number of slices to approximately accommodate for the differences, but it still isn't working. Any help would be appreciated. The density relative to the bilayer center is much more useful than trying to manipulate the box directly. This is what the -center and -symm options are for. See the complete description in the help text. Centering on the bilayer itself in each case should resolve your problem. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] lipid pulling
On 7/6/16 7:24 AM, xy21hb wrote: Dear all, I am pulling the saturated and unsaturated chains of a lipid bilayer to "simulate" its gel phase transition by pull code. It ends with the expected extended structure. But when I continue with zero pulling rate to maintain the extended structure for a while, the tails go back to the original length. I guess I have made some mistakes in the mdp pull code part, = pull= umbrella pull-ngroups= 6 pull-ncoords= 4 pull-group1-name= topC2 pull-group2-name= downC2 pull-group3-name= topC218 pull-group4-name= downC218 pull-group5-name= topC316 pull-group6-name= downC316 pull-geometry= distance ; simple distance increase pull-coord1-groups = 1 3 pull-coord2-groups = 1 5 pull-coord3-groups = 2 4 pull-coord4-groups = 2 6 pull-dim = N N Y pull-coord1-vec = 0 0 1 pull-coord1-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns pull-coord1-k = 1000 ; kJ mol^-1 nm^-2 pull-coord2-vec = 0 0 1 pull-coord2-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns pull-coord2-k = 1000 ; kJ mol^-1 nm^-2 pull-coord3-vec = 0 0 1 pull-coord3-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns pull-coord3-k = 1000 ; kJ mol^-1 nm^-2 pull-coord4-vec = 0 0 1 pull-coord4-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns pull-coord4-k = 1000 ; kJ mol^-1 nm^-2 pull-coord1-init= 1.0 pull-coord2-init= 1.0 pull-coord3-init= 1.0 pull-coord4-init= 1.0 pull-start = yes ; define initial COM distance > 0 Any guess on the reason? Many thanks. You should use pull-start = yes and not use pull-coord*-init if the lipids are already in the configuration you want. Otherwise, you're trying to set the starting distance + 1.0 nm as the reference, which may not be physically possible or sensible. -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] Ligand hybridization
On 7/6/16 12:26 PM, Chetan Puri wrote: I am confused with the fact that after processing ligand through prodrg whatever pdb file you get it doesn't show aromatic ring double bonds( if we view it using pymol or vmd) And I don't understand that although it shows aromatic ring planar but no double bonds are present. So is it the way aromatic ring is supposed to be after passing through prodrg. It has nothing to do with PRODRG (which hopefully you aren't using for topologies, unless you're manually correcting them) and everything to do with the visualization software. Most programs don't explicitly render double bonds, anyway. -Justin On 5 Jul 2016 10:26 pm, "Justin Lemkul" wrote: On 7/5/16 10:50 AM, Chetan Puri wrote: I am trying to do a protein- ligand simulation. And the prodrg server provides the ligand out put by completely removing the double bonds(making it saturated) So is there any way to do it. See the PRODRG FAQ for dealing with incorrect protonation. Then make sure you fix the PRODRG topology because the charges won't be right. Or use a better server like ATB. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem in umbrella sampling for PMF calculation
On 7/6/16 11:13 AM, Shi Li wrote: Dear GMX users, I am a beginner of Gromacs and I am trying to calculate the potential of mean force in my simulation system. In my simulation box I have two small molecules(70 atoms each). I am fixing one molecule and moving the other approaching to it along Z axis. I use following .mdp code to push these two molecules together. --- title = Umbrella pulling simulation define = -DPOSRES_B ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 nstvout = 5000 nstfout = 500 nstxtcout = 500 nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; Single-range cutoff scheme cutoff-scheme = group nstlist = 1 ns_type = grid nstcalclr=1 rlist = 0 rcoulomb= 0 rvdw= 0 ;; PME electrostatics parameters coulombtype = cut-off fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Berendsen tc_grps = System tau_t = 0.5 ref_t = 310 ; Pull code pull = umbrella pull_geometry= distance; pull_dim = N N Y pull_start = yes pull-ncoords = 1 pull_ngroups = 2 pull_group1_name = core2; moving molecule pull_group2_name = core1; fixed molecule pull-coord1-groups = 2 1 pull_coord1_init = 3 pull_coord1_rate = 0.005 pull_coord1_k = 100 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps ;--- After the pushing process, I selected the configurations(0.2 nm each) from the result and did the equilibrium and umbrella sampling with following mdp files. (Equilibrium) title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 5000 nstcomm = 10 ; Output parameters nstxout = 500 ; nstvout = 500 nstfout = 500 nstxtcout = 500 s nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= no ; Single-range cutoff scheme nstlist = 1 cutoff-scheme = group ns_type = grid rlist = 0 rcoulomb= 0 rvdw= 0 ;; PME electrostatics parameters coulombtype = cut-off fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Berendse tc_grps = System tau_t = 0.5 ref_t = 310 ; Pull code pull = umbrella pull_geometry= distance pull_dim = N N Y pull_start = yes pull-ncoords = 1 pull_ngroups = 2 pull_group1_name = core2 pull_group2_name = core1 pull-coord1-groups = 1 2 pull_coord1_rate = 0.0 pull_coord1_k = 100 pull_nstxout= 1000 pull_nstfout= 1000 ; (Umbrella sampling): title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.001 tinit = 0 nsteps = 500 nstcomm = 10 ; Output parameters nstxout = 5 nstvout = 5 nstfout = 5000 nstxtcout = 5000 nstenergy = 5000 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; Single-range cutoff scheme cutoff-scheme = group nstlist = 5 ns_type = grid rlist = 0 rcoulomb= 0 rvdw= 0 ; PME electrostatics parameters coulombtype = cut-off fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Berendsen tc_grps = System tau_t = 0.5 ref_t = 310 pull = umbrella pull_geometry= distance pull_dim = Y Y Y pull_start = yes pull-ncoords = 1 pull_ngroups = 2 pull_group1_name = core2 pull_group2_name = core1 pull-coord1-groups = 1 2 pull_coord1_rate = 0.0 pull_coord1_k = 100 pull_nstxout= 1000 pull_nstfout= 1000 -- After these, I did WHAM to generate the profile file and plot it. I got a curve went from 0 to negative as the distance increase, which didn't seem to be correct. My questions are: 1, What is wrong with my input mdp files? What should I change in the mdp files for a simple simulation system in vacuum? Don't use position restraints. This is probably completely undermining your entire process. 2. Is the profile.xvg file generated from WHAM directly plotable? Or should I do some modification before ploting it? It's the result you need. 3. I thought the PMF should go close to zero as the distance increase, should I manual set a referen
Re: [gmx-users] Analyzing With Indices Created By GMX Select
On 7/6/16 2:41 PM, ALEXANDER DHALIWAL wrote: Hi All, I am having a problem. Using GMX Select, I have selected for some molecules within my simulation; namely, a solute of interest and the phospholipids surrounding it within a radius of 2 nm. This was done using the following command: gmx select -f md_2_25_cat.trr -s md_2_25_cat.tpr -n all_groups.ndx -on select.ndx ... group 5 group 7 and within 2 of resid 138 ctrl+D This generates an index file with an independent group for every frame of my simulation, as the molecules contained within this designation change as time goes on. However, I am now unsure about how to use this index file in any analyses. For instance, if I want to calculate the hydrogen bonds between this group and the surrounding solvent, is there a way to assign a new pairs of groups for every frame of the simulation (i.e., group SOL + group Fr1 for Frame 1; group SOL + group Fr2 for Frame 2, etc)? Currently, I can only compare it to a single frame group, and this isn't very helpful. If anyone can help me with this, it would be much appreciated! Dynamic indices are not smoothly integrated into most analysis programs yet, so frame-by-frame is the only way to go in most instances. Easily done with a loop in a shell script. -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] Calculation of non bonded interaction
On 7/7/16 7:26 AM, Praveen Kumar wrote: Hi, I want to calculate non bonded interaction between an ion pair (say "A" and "B"). There are total 125 ion pairs in the system. How could I calculate the average non bonded interaction between one cation and anion in the system? Set appropriate energygrps in the .mdp file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to build caps for my peptide termini?
Dear All, I want to cap the ends of my peptide chain. Though -ter option of pdb2gmx takes up its zwitterionic form quite easily, I've read somewhere that termini are quite mobile and it is better to proceed with capping. I want to use GROMOS53a6 parameters and I've found entries of ACE and NAC in its .rtp file. My dilemma is how to build caps onto my pdb file? What about their coordinates? Where should I insert them? I tried building it using pymol but it didn't work. Some softwares like Schrodinger's Protein Preparation Wzard is great with stuff like this but I don't have the resources to buy paid software. Could you please suggest a way how to do this? Here are some of the coordinates Starting residue: ATOM 1 N GLN A 1 7.066 21.384 0.641 1.00 11.02 N ATOM 2 CA GLN A 1 5.949 20.973 1.534 1.00 10.36 C ATOM 3 C GLN A 1 5.275 19.686 1.047 1.00 9.45 C ATOM 4 O GLN A 1 5.014 18.782 1.840 1.00 9.34 O ATOM 5 CB GLN A 1 4.928 22.115 1.616 1.00 10.69 C ATOM 6 CG GLN A 1 3.676 21.765 2.403 1.00 11.26 C ATOM 7 CD GLN A 1 3.987 21.223 3.784 1.00 11.68 C ATOM 8 OE1 GLN A 1 3.745 20.021 4.019 1.00 11.97 O ATOM 9 NE2 GLN A 1 4.475 22.002 4.632 1.00 11.90 N ATOM 10 H1 GLN A 1 7.823 21.771 1.239 1.00 11.21 H ATOM 11 H2 GLN A 1 6.702 22.105 -0.016 1.00 11.26 H ATOM 12 H3 GLN A 1 7.392 20.540 0.130 1.00 11.19 H ATOM 13 HA GLN A 1 6.354 20.797 2.521 1.00 10.53 H ATOM 14 HB2 GLN A 1 5.397 22.965 2.088 1.00 10.93 H ATOM 15 HB3 GLN A 1 4.631 22.391 0.615 1.00 10.52 H ATOM 16 HG2 GLN A 1 3.073 22.656 2.510 1.00 11.34 H ATOM 17 HG3 GLN A 1 3.119 21.019 1.857 1.00 11.54 H Ending residue ATOM475 N LEU A 33 -9.783 -18.497 -1.487 1.00 5.97 N ATOM476 CA LEU A 33 -10.736 -19.453 -0.936 1.00 6.85 C ATOM477 C LEU A 33 -10.018 -20.571 -0.187 1.00 7.51 C ATOM478 O LEU A 33 -10.708 -21.452 0.366 1.00 7.81 O ATOM479 CB LEU A 33 -11.601 -20.043 -2.052 1.00 7.27 C ATOM480 CG LEU A 33 -12.071 -19.040 -3.107 1.00 7.87 C ATOM481 CD1 LEU A 33 -12.991 -19.715 -4.113 1.00 8.08 C ATOM482 CD2 LEU A 33 -12.773 -17.862 -2.446 1.00 8.48 C ATOM483 OXT LEU A 33 -8.769 -20.557 -0.163 1.00 7.98 O ATOM484 H LEU A 33 -9.837 -17.556 -1.214 1.00 5.99 H ATOM485 HA LEU A 33 -11.373 -18.923 -0.242 1.00 7.08 H ATOM486 HB2 LEU A 33 -11.031 -20.815 -2.548 1.00 7.07 H ATOM487 HB3 LEU A 33 -12.473 -20.495 -1.604 1.00 7.69 H ATOM488 HG LEU A 33 -11.213 -18.661 -3.642 1.00 8.04 H ATOM489 HD11 LEU A 33 -12.516 -20.606 -4.494 1.00 8.27 H ATOM490 HD12 LEU A 33 -13.192 -19.036 -4.928 1.00 8.16 H ATOM491 HD13 LEU A 33 -13.920 -19.979 -3.629 1.00 8.27 H ATOM492 HD21 LEU A 33 -12.052 -17.087 -2.232 1.00 8.84 H ATOM493 HD22 LEU A 33 -13.234 -18.189 -1.527 1.00 8.47 H ATOM494 HD23 LEU A 33 -13.531 -17.476 -3.112 1.00 8.84 H yours sincerely Apramita -- 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] lipid pulling
Dear all, Sorry, I realized that. It is just I forgot to delete the pull-coord-init part. But after I delete the followinf lines, === >> pull-coord1-init= 1.0 >> pull-coord2-init= 1.0 >> pull-coord3-init= 1.0 >> pull-coord4-init= 1.0 >> == and keep the " pull-start = yes " The problem remains. Any new idea on that? Thanks, Yao At 2016-07-07 19:43:54, "Justin Lemkul" wrote: > > >On 7/6/16 7:24 AM, xy21hb wrote: >> Dear all, >> >> I am pulling the saturated and unsaturated chains of a lipid bilayer to >> "simulate" its gel phase transition by pull code. It ends with the expected >> extended structure. >> >> But when I continue with zero pulling rate >> to maintain the extended structure for a while, the tails go back to the >> original length. >> I guess I have made some mistakes in the mdp pull code part, >> >> = >> pull= umbrella >> pull-ngroups= 6 >> pull-ncoords= 4 >> >> pull-group1-name= topC2 >> pull-group2-name= downC2 >> pull-group3-name= topC218 >> pull-group4-name= downC218 >> pull-group5-name= topC316 >> pull-group6-name= downC316 >> >> pull-geometry= distance ; simple distance increase >> >> pull-coord1-groups = 1 3 >> pull-coord2-groups = 1 5 >> pull-coord3-groups = 2 4 >> pull-coord4-groups = 2 6 >> pull-dim = N N Y >> >> pull-coord1-vec = 0 0 1 >> pull-coord1-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns >> pull-coord1-k = 1000 ; kJ mol^-1 nm^-2 >> pull-coord2-vec = 0 0 1 >> pull-coord2-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns >> pull-coord2-k = 1000 ; kJ mol^-1 nm^-2 >> pull-coord3-vec = 0 0 1 >> pull-coord3-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns >> pull-coord3-k = 1000 ; kJ mol^-1 nm^-2 >> pull-coord4-vec = 0 0 1 >> pull-coord4-rate= 0.000 ; 0.01 nm per ps = 10 nm per ns >> pull-coord4-k = 1000 ; kJ mol^-1 nm^-2 >> >> pull-coord1-init= 1.0 >> pull-coord2-init= 1.0 >> pull-coord3-init= 1.0 >> pull-coord4-init= 1.0 >> >> pull-start = yes ; define initial COM distance > 0 >> >> >> >> Any guess on the reason? Many thanks. >> > >You should use pull-start = yes and not use pull-coord*-init if the lipids are >already in the configuration you want. Otherwise, you're trying to set the >starting distance + 1.0 nm as the reference, which may not be physically >possible or sensible. > >-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.
Re: [gmx-users] mdrun rerun to large frame numbers
Hi, On 07/07/2016 12:53 PM, Mark Abraham wrote: Hi, Hmm, that sounds like your very long trajectory is running into some integer exceeding its maximum size. mdrun proper uses a 64-bit integer for step number, but doubtless there are dusty corners. Are you able to estimate which frame number this was? It seems to be a problem of the step number (around 2e+9) to make the trouble. What does gmx check say about the very long trajectory? gmx check works fine. Giving all the outputs I am used to like: Step 50 Coords 50 no trouble. To work around it, you can probably just use gmx trjconv to break the trajectory into parts, but we'd rather find the problem and fix it :-) I tried this now it always works for the first half but not for the second. Is there a way to change the step number? Since the frame number does not seem to produce the error. Mark Thanks, Basti On Thu, Jul 7, 2016 at 11:59 AM Sebastian < sebastian.buchenb...@physik.uni-freiburg.de> wrote: Hey, I try to perform an rerun of very long trajectories using mdrun. The problem is, that the rerun crashes after it reaches a certain frame number with the warning: there may be something wrong with the energy file XXX.edr Found: step=-1983077269, nre=49, nblock=0, time=4.62378e+06. Trying to skip frame expect a crash though. I tried it for three different runs and I get always the same warning. The step number is something strange. Best, Basti -- 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] mdrun rerun to large frame numbers
Hi, On Thu, Jul 7, 2016 at 3:17 PM Sebastian < sebastian.buchenb...@physik.uni-freiburg.de> wrote: > Hi, > > On 07/07/2016 12:53 PM, Mark Abraham wrote: > > Hi, > > > > Hmm, that sounds like your very long trajectory is running into some > > integer exceeding its maximum size. mdrun proper uses a 64-bit integer > for > > step number, but doubtless there are dusty corners. Are you able to > > estimate which frame number this was? > > It seems to be a problem of the step number (around 2e+9) to make the > trouble. > A signed 32-bit integer indeed has a range up to +2e+9, so that confirms my suspicion. > What does gmx check say about the > > very long trajectory? > > gmx check works fine. Giving all the outputs I am used to like: > > Step 50 > Coords 50 > > no trouble. > > > To work around it, you can probably just use gmx > > trjconv to break the trajectory into parts, but we'd rather find the > > problem and fix it :-) > > I tried this now it always works for the first half but not for the second. > Shucks. However, that makes me expect that you can probably reproduce the problem with a very short piece of trajectory that includes a step number > 2^31 = 2147483648. If so, please mail me that trajectory + .tpr + failing .log file and I can probably fix it quickly once I find which bit is failing. Is there a way to change the step number? Since the frame number does > not seem to produce the error. > I'm not aware of a mechanism, and a quick glance at the code of trjconv and trjcat didn't suggest anything. I had an idea that gmx trjcat -settime on the second half might be useful, but I now doubt it will work. Mark > > > Mark > > > Thanks, > > Basti > > > > > > On Thu, Jul 7, 2016 at 11:59 AM Sebastian < > > sebastian.buchenb...@physik.uni-freiburg.de> wrote: > > > >> Hey, > >> > >> I try to perform an rerun of very long trajectories using mdrun. > >> The problem is, that the rerun crashes after it reaches a certain frame > >> number with the warning: > >> > >> there may be something wrong with the energy file XXX.edr > >> Found: step=-1983077269, nre=49, nblock=0, time=4.62378e+06. > >> Trying to skip frame expect a crash though. > >> > >> I tried it for three different runs and I get always the same warning. > >> The step number is something strange. > >> > >> Best, > >> > >> Basti > >> -- > >> 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] Problem with Group and Verlet cut -off scheme
Dear Gromacs users, Thank you very reading. I am trying to run a simulation that requires me to use lennard jones and buckingham potential mix, thus I have to make my own tabulated table .xvg list. However here is my problem, because Verlet does not support tabulated table so I have to use group scheme. But here is the error message I am getting : Fatal error: The largest charge group contains 574 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors My simulation is a single crystal structure. Thus my question is: 1) is it possible to change the charge group? if so, how? as I read the manual seems it is not possible. 2) if I am using tabulated table, do I have to make a .xvg file for all interacting molecule (because I just need to change one interaction into buckingham potential) Thank you very much. Best regards, Ben -- 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] Surface tension calculation for organic monolayer
Dear users, I simulated three different systems in cubic box and calculated their surface tension as shown below; 1. Pure water , surface tension = 61.5 mN/m 2. Water with 3M NaCl salt, surface tension = 66.5 mN/m 3.Water surface covered with cis-pinonic organic, surface tension = 63.5 mN/m For system 1 and 2, the results are almost correct however the result for system 3 is not correct. Cis-pionic is an surface active molecule and should lower the surface tension. However in my simulations I could not capture this trend. I used GAFF force field and LINCS for the constraints. Does anyone has any idea? Or is there anyone that calculated the surface tension for organic coated surfaces with GAFF force field? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem with Group and Verlet cut -off scheme
Hi, On Thu, Jul 7, 2016 at 3:44 PM Ben Tam wrote: > Dear Gromacs users, > > > Thank you very reading. I am trying to run a simulation that requires me > to use lennard jones and buckingham potential mix, That's often tricky to get right, because you still need VDW combination rules that work for all pairs of atom types that might be within an interaction radius (and probably slightly breaks any dispersion correction also). Then you have to express that as energy groups to get the tables to work (without running out of energy groups, IIRC max 128). thus I have to make my own tabulated table .xvg list. However here is my > problem, because Verlet does not support tabulated table so I have to use > group scheme. But here is the error message I am getting : > > > Fatal error: > The largest charge group contains 574 atoms. The maximum is 32. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > My simulation is a single crystal structure. Thus my question is: > > > 1) is it possible to change the charge group? if so, how? as I read the > manual seems it is not possible. > You specified the charge groups in your molecule's [atoms] section, so you can select a different setup, e.g. one charge group per atom (and your neighbourlist should likely be set up to have a buffer) > 2) if I am using tabulated table, do I have to make a .xvg file for all > interacting molecule (because I just need to change one interaction into > buckingham potential) > For historical reasons, each energygroup pair needs to either use the default interaction type, or replaced with a table. Mark > Thank you very much. > > > Best regards, > > > Ben > -- > 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] gmx_saxs sampling frequency
Hello, I am attempting to use the gmx_saxs tool in order to resolve the x-ray scattering intensity profile for a trajectory of aggregating molecules. The primary peaks (non-log scale) are occurring at q values of about 0.5 1/nm. Unfortunately, the gmx_saxs tool doesn't have a feature to decrease the grid spacing in q-space. Does anyone know if there is a way to make tool calculate with more resolution in the small q range (preferably without diving into and modifying the module)? Any ideas would be much appreciated. Thanks, Evan L. -- 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] Surface tension calculation for organic monolayer
On 07/07/16 16:06, gozde ergin wrote: Dear users, I simulated three different systems in cubic box and calculated their surface tension as shown below; 1. Pure water , surface tension = 61.5 mN/m 2. Water with 3M NaCl salt, surface tension = 66.5 mN/m 3.Water surface covered with cis-pinonic organic, surface tension = 63.5 mN/m For system 1 and 2, the results are almost correct however the result for system 3 is not correct. Cis-pionic is an surface active molecule and should lower the surface tension. However in my simulations I could not capture this trend. I used GAFF force field and LINCS for the constraints. Does anyone has any idea? Or is there anyone that calculated the surface tension for organic coated surfaces with GAFF force field? Thanks Maybe you should consider pH effects? Since this is an acid I would guess part of these are deprotonated in solution, did you consider the pK? You probably need to mix different amounts of protonated and deprotonated molecules and plot the surface tension as a function of the protonation state. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Residue Numbers
Dear All, I used g_mmpbsa for free energy calculations. I competed contribution of residues to the binding energy using python script. Original residue number is available in final_contrib_energy.dat file. But we use energyMapIn.dat file for the graph plotting. In that file residue numbers are different, it always start with number one. How can I plot residue number vs energy contribution? Can anyone help me? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Surface tension calculation for organic monolayer
Dear Spoel, Thanks for your respond. For this simulations I used acids however I got the similar results when I used alcohol (pK values are lower than acids). I doubt this error coming from the pH effects. But how could i get the protonated molecules configuration? > On 07 Jul 2016, at 17:11, David van der Spoel wrote: > > On 07/07/16 16:06, gozde ergin wrote: >> Dear users, >> >> I simulated three different systems in cubic box and calculated their >> surface tension as shown below; >> >> 1. Pure water , surface tension = 61.5 mN/m >> 2. Water with 3M NaCl salt, surface tension = 66.5 mN/m >> 3.Water surface covered with cis-pinonic organic, surface tension = 63.5 mN/m >> >> For system 1 and 2, the results are almost correct however the result for >> system 3 is not correct. >> >> Cis-pionic is an surface active molecule and should lower the surface >> tension. >> However in my simulations I could not capture this trend. >> I used GAFF force field and LINCS for the constraints. >> Does anyone has any idea? >> Or is there anyone that calculated the surface tension for organic coated >> surfaces with GAFF force field? >> >> Thanks >> > Maybe you should consider pH effects? Since this is an acid I would guess > part of these are deprotonated in solution, did you consider the pK? You > probably need to mix different amounts of protonated and deprotonated > molecules and plot the surface tension as a function of the protonation state. > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > -- > 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] Surface tension calculation for organic monolayer
Few things to check: Do you observe that the cis-pinonic acid or alcohol forms a monolayer at the water-vacuum interface? If yes, are solvation energies considered in the force filed development for this organic molecule (that can make the difference) An example of where we observed "http://pubs.acs.org/doi/abs/10.1021/la904615u"; On Thu, Jul 7, 2016 at 11:51 AM, gozde ergin wrote: > Dear Spoel, > Thanks for your respond. > For this simulations I used acids however I got the similar results when I > used alcohol (pK values are lower than acids). > I doubt this error coming from the pH effects. > But how could i get the protonated molecules configuration? > > On 07 Jul 2016, at 17:11, David van der Spoel > wrote: > > > > On 07/07/16 16:06, gozde ergin wrote: > >> Dear users, > >> > >> I simulated three different systems in cubic box and calculated their > surface tension as shown below; > >> > >> 1. Pure water , surface tension = 61.5 mN/m > >> 2. Water with 3M NaCl salt, surface tension = 66.5 mN/m > >> 3.Water surface covered with cis-pinonic organic, surface tension = > 63.5 mN/m > >> > >> For system 1 and 2, the results are almost correct however the result > for system 3 is not correct. > >> > >> Cis-pionic is an surface active molecule and should lower the surface > tension. > >> However in my simulations I could not capture this trend. > >> I used GAFF force field and LINCS for the constraints. > >> Does anyone has any idea? > >> Or is there anyone that calculated the surface tension for organic > coated surfaces with GAFF force field? > >> > >> Thanks > >> > > Maybe you should consider pH effects? Since this is an acid I would > guess part of these are deprotonated in solution, did you consider the pK? > You probably need to mix different amounts of protonated and deprotonated > molecules and plot the surface tension as a function of the protonation > state. > > > > -- > > David van der Spoel, Ph.D., Professor of Biology > > Dept. of Cell & Molec. Biol., Uppsala University. > > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. > > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > > -- > > 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. > -- Naga Rajesh Tummala -- 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] Surface tension calculation for organic monolayer
On 07/07/16 17:51, gozde ergin wrote: Dear Spoel, Thanks for your respond. For this simulations I used acids however I got the similar results when I used alcohol (pK values are lower than acids). I doubt this error coming from the pH effects. But how could i get the protonated molecules configuration? Just add a Hydrogen and update the topology. For sure you won't have 100% of COO- if you have many. As Naga mentioned you have to check surface propensity and compare it to experimental data if you have any. This - again - is modulated by the charge state. The only way to do this kind of calculations in a meaningful way is by doing series of calculations as I alluded to. Just a single calculation can be a lucky shot. On 07 Jul 2016, at 17:11, David van der Spoel wrote: On 07/07/16 16:06, gozde ergin wrote: Dear users, I simulated three different systems in cubic box and calculated their surface tension as shown below; 1. Pure water , surface tension = 61.5 mN/m 2. Water with 3M NaCl salt, surface tension = 66.5 mN/m 3.Water surface covered with cis-pinonic organic, surface tension = 63.5 mN/m For system 1 and 2, the results are almost correct however the result for system 3 is not correct. Cis-pionic is an surface active molecule and should lower the surface tension. However in my simulations I could not capture this trend. I used GAFF force field and LINCS for the constraints. Does anyone has any idea? Or is there anyone that calculated the surface tension for organic coated surfaces with GAFF force field? Thanks Maybe you should consider pH effects? Since this is an acid I would guess part of these are deprotonated in solution, did you consider the pK? You probably need to mix different amounts of protonated and deprotonated molecules and plot the surface tension as a function of the protonation state. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] binding free energy
Hi Justin, The free ligand is the ligand in a box of solvent, and the complex is the complex in a box of solvent. The complex would need to exist for the duration of each of your lambda windows for this method to be reliable, and the system would need to be in equilibrium as well... Have you considered steered MD? I would imagine that you will need pull code constraints holding your amino acid in place as the VDW and coulomb lambdas get close to 1. However if you are performing a relative FEP calculation, you can probably avoid using restraints depending on whether State B still interacts with the ionic surface. You also may or may not find that you will need more coulomb lambdas depending on how long each window is being simulated for. You don't need a temperature lambda setting as you are not perturbing the temperature, I don't think? Mass lambdas are unnecessary because you should not be perturbing the mass either in an absolute FEP run. They are still unnecessary in a relative run since the mass contributions should cancel in a closed thermodynamic cycle. If you are perturbing dihedral angles though, maybe consider using the FEP-lambdas setting. Hope you've been going well! :) Also, this would be my approach. I know absolute and relative FEP methods work well for ligands binding to proteins, but I have no experience with the exact situation that you're describing. Good luck! Billy On 5 July 2016 at 19:09, Alexander Alexander wrote: > Hello Billy, > > Thanks for your response. > > Please confirm me that with bonded(complex), you mean the geometry of > "amino acid+solidsurface+ water" that I should harvest in advance by normal > MD simulation in which amino acid has been absorbed into the surface. and > then this geometry should be used as the initial structure for each lambda > in order to do FEP. > > Also, what do you mean please by the free (unbound)? If it is a geometry of > again "amino acid+solidsurface+ water" in which amino acid has been > solvated in water far away from the solid surface? or just an amino acid > solvated in a box of water without solid surface (amino acid + water). > > Good to know that this strategy is the one mentioned in below paper (Figure > 1): > http://pubs.acs.org/doi/full/10.1021/ct400487e > > Here is the free energy parameter I am using in my calculation would you > please comment on it, or let me know if I should consider any other > parameter changes like mass-restrain-tempetatre-lambda? > > free-energy = yes > init-lambda-state = MYLAMBDA ;;;from (i=0;i<15;i++) > calc-lambda-neighbors= -1 > vdw-lambdas = 0.00 0.00 0.00 0.00 0.00 0.10 0.20 0.30 0.40 > 0.50 0.60 0.70 0.80 0.90 1.00 > coul-lambdas = 0.00 0.25 0.50 0.75 1.00 1.00 1.00 1.00 1.00 > 1.00 1.00 1.00 1.00 1.00 1.00 > couple-moltype= Protein_chain_A > couple-lambda0 = vdw-q > couple-lambda1 = none > couple-intramol = no > nstdhdl = 50 > sc-alpha= 0.5 > sc-coul = no > sc-power= 1 > sc-sigma= 0.3 > > > Thanks. > Regards, > Alex > > > > > On Tue, Jul 5, 2016 at 3:03 AM, Billy Williams-Noonan < > billy.williams-noo...@monash.edu> wrote: > > > Just to clarify, the formula should be: > > > >dG (bind) = dG (complex) - dG (solv) > > > > Billy > > > > On Tuesday, 5 July 2016, Billy Williams-Noonan < > > billy.williams-noo...@monash.edu> wrote: > > > > > You would want to perturb your amino acid in both the free (unbound) > and > > > complex (bound) aqueous states. > > > > > > Then if you subtract the free energy change from perturbing the free > > > ligand, from that of perturbing the bound ligand, you should close the > > > non-physical thermodynamic cycle and get a binding free energy. > > > > > > But you will need to make sure everything in your simulation is > > > parameterised properly to get an accurate value. You will also need to > > > make sure you have sufficient sampling time and lambda states. > > > > > > Good luck! > > > > > > Billy > > > > > > On Tuesday, 5 July 2016, Alexander Alexander < > alexanderwie...@gmail.com> > > > wrote: > > > > > >> Dear gromacs user, > > >> > > >> I was wondering if anybody has any experience with binding free energy > > >> calculation of a molecule (here amino acid) into a solid surface in > > >> aqueous > > >> solution using alchemical analysis? > > >> > > >> I have already tried successfully the tutorial of methane solvation > free > > >> energy in water and some other examples, but looks all of them are > > >> solvation free energy and not binding free energy! > > >> > > >> Thanks. > > >> Regards, > > >> Alex > > >> -- > > >> 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.
[gmx-users] new residue went into crash during energy minimization
Hello,everyone! I am using charmm27 in gromacs for simulation of a double strand DNA , of which a residue is modified by a group.The forcefield parameters for the new residue is generated with swissparam. After conducting energy minimization , i checked the DNA's structure with pymol . Obviously , some thing is wrong . Except for the atoms in the back bone , all the atoms in the modified residue are seperated from each other . What can i do to make it though the energy minimization? Thank you! Tao Wang -- 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] Position restraints for water during EM
Hello all: I would like to know where it is specified that waters are position-restrained during energy minimization. I can see that there is a #ifdef block for restraining the water, but I don't know where it is actually called. The .mdp files I use for EM (which I adapted from tutorials) do not make DEFINE statements, and I also don't see any DEFINE statements for DPOSRES_WATER in the mdout.mdp file. Thanks in advance for pointing me in the right direction. Gregory -- 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.
