Re: [gmx-users] Fwd: geometry optimization of metalloenzyme
On 4/9/20 4:25 PM, Nadia Elghobashi-Meinhardt wrote: Thank you, Justin. I am still struggling with constraints. I am trying to use "freezegrps" and "freezedim" to run an NVT equilibration. However, when I try to build the binary using my optimized structure, I get either "Segmentation fault" or the following error: "free(): invalid next size (fast) Aborted" What do these messages indicate? Problem in memory allocation? All of this is probably a downstream effect of a simulation that is unstable and crashed. Freezing is totally artificial and I strongly discourage using it. The crash may be due to failure to use energygrp_exclusions when freezing or due to intrinsic instability of the system that even freezing cannot overcome. -Justin On Thu, Apr 2, 2020 at 9:26 PM Justin Lemkul wrote: On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote: Hello everyone, I am trying to minimize the potential energy of a metalloenzyme containing Ni and Fe atoms. What is the best way to constrain (fix?) the position of the active site atoms during the geometry optimization? I have tried introducing bonds with relatively high force constants and alternatively, tried introducing a [constraints] section, but the atoms are still not staying put. Bonds or constraints will maintain distances between atoms (relative position) but not absolute position. Or should one use extra position restraints? If the absolute position matters, yes. I would think the approach of adding restraints or constraints between atoms would be more meaningful given that preserving coordination geometry is often the defect in MM treatment of transition metals. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] dt in mdp
On 4/10/20 8:13 AM, Alex wrote: Dear Justin, Any comment please? Sorry, haven't had power/network for a while due to some bad storms here. GROMOS force fields are parametrized assuming all bonds are fixed, so your constraints should be "all-bonds" not "h-bonds." I would also suggest you thoroughly validate the quality of the epoxy molecule topology against QM data and bulk-phase properties, if possible. -Justin Regards, Alex On Tue, Apr 7, 2020 at 5:38 PM Alex wrote: Thanks Justin for the response. Please find below the mdp file. The system is a thin film made out of a epoxy molecule, picture in be below link, with water on top and bottom of the film. I even sometimes have the same issue when I simulate the bulk of this system, I mean a cubic box filled by this molecule and no water. I got the force fields from the latest version of ATB repository by which I have previously done some other simulation for the same molecule. https://drive.google.com/open?id=1tJLxh9jQ2v5DDTrVR8IuQz40B3NN0zlb %mdp--- title= Thin-Film integrator = md dt = 0.002 ; 2 fs ;0.001 1 fs nsteps = 2500 ; 50 ns ;5000 ; 50 ns xtc-precision= 500 ; 1000 ;nstlist = 40 %- ;;in .trr file nstxout = 3000 ; 6000 nstvout = 0 nstfout = 0 ;;in energy file.log nstlog = 2000 ; 4000 nstcalcenergy= 2000 ;4000 nstenergy= 2000 ;4000 ;;in xtc file nstxout-compressed = 0 ;compressed-x-grps= non-Water %- continuation = yes gen-vel = no constraint-algorithm = lincs constraints = h-bonds cutoff-scheme= Verlet coulombtype = PME rcoulomb = 1.4 vdwtype = Cut-off rvdw = 1.4 DispCorr = EnerPres tcoupl= v-rescale tc-grps = system tau-t = 1.5 nhchainlength = 10 ref-t = 298.15 pbc = xyz pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p= 2.5 compressibility = 4.5e-5 ref_p= 1.0 refcoord-scaling = com energygrps = thin_film SOL comm-mode= Linear nstcomm = 100 comm-grps= Thin_fiml SOL %- Thank you Alex On Tue, Apr 7, 2020 at 5:06 PM Justin Lemkul wrote: On 4/7/20 5:00 PM, Alex wrote: Dear all, After minimization and equalizations using nvt (v-rescale) and npt (both berendsen and ;Parrinello-Rahman), a simulation of mine could run well for 200 ns using dt =0.001 while it would crash after 3 ns If I used dt = 0.002 with the particles communication fatal error. Fatal error: 2 particles communicated to PME rank 12 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. So, if the system would not be well equlibrated, then I would expect that with dt = 0.001 the simulation wouldn't run well for 200 ns. But I expect that it also crashes for example around 6 ns as the with the dt = 0.002 the simulation last only 3 ns. Any comment that helps to understand the problem would be highly appreciated. Please provide a description of what your system is and a full .mdp file. While most of the time these crashes come from poor equilibration, an inadequately parametrized topology or bad combination/misuse of algorithms can also cause crashes. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] dt in mdp
On 4/10/20 9:16 AM, Alex wrote: Thank you for the response. On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: On 4/10/20 8:13 AM, Alex wrote: Dear Justin, Any comment please? Sorry, haven't had power/network for a while due to some bad storms here. GROMOS force fields are parametrized assuming all bonds are fixed, so your constraints should be "all-bonds" not "h-bonds." Interesting, hopefully that is the problem. I would also suggest you thoroughly validate the quality of the epoxy molecule topology against QM data and bulk-phase properties, if possible. As the ATB folks claim, the parameterization has been performed against a very high level DFT calculation, especially for the molecules with less than 50 atoms. I already have tested the density and it is in agreement with the experimental value. Regarding the "comm-grps = " , would you also please kindly let me know which one you would recommend for this system + plus a small single molecule called MOL_A which defuses from water inside the epoxy, specially for the PMF calculation of the Mol_A? comm-grps = Other SOL ;; (Other = thin_film and Mol_A) or comm-grps = system I saw the conversation with David about this. I have nothing to add that he hasn't already said. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] dt in mdp
Dear Justin, Any comment please? Regards, Alex On Tue, Apr 7, 2020 at 5:38 PM Alex wrote: > Thanks Justin for the response. > Please find below the mdp file. > The system is a thin film made out of a epoxy molecule, picture in be > below link, with water on top and bottom of the film. I even sometimes have > the same issue when I simulate the bulk of this system, I mean a cubic box > filled by this molecule and no water. > I got the force fields from the latest version of ATB repository by which > I have previously done some other simulation for the same molecule. > > https://drive.google.com/open?id=1tJLxh9jQ2v5DDTrVR8IuQz40B3NN0zlb > > %mdp--- > title= Thin-Film > integrator = md > dt = 0.002 ; 2 fs ;0.001 1 fs > nsteps = 2500 ; 50 ns ;5000 ; 50 ns > xtc-precision= 500 ; 1000 > ;nstlist = 40 > %- > ;;in .trr file > nstxout = 3000 ; 6000 > nstvout = 0 > nstfout = 0 > ;;in energy file.log > nstlog = 2000 ; 4000 > nstcalcenergy= 2000 ;4000 > nstenergy= 2000 ;4000 > ;;in xtc file > nstxout-compressed = 0 > ;compressed-x-grps= non-Water > %- > continuation = yes > gen-vel = no > constraint-algorithm = lincs > constraints = h-bonds > cutoff-scheme= Verlet > coulombtype = PME > rcoulomb = 1.4 > > vdwtype = Cut-off > rvdw = 1.4 > DispCorr = EnerPres > > tcoupl= v-rescale > tc-grps = system > tau-t = 1.5 > nhchainlength = 10 > ref-t = 298.15 > pbc = xyz > > pcoupl = Parrinello-Rahman > Pcoupltype = isotropic > tau_p= 2.5 > compressibility = 4.5e-5 > ref_p= 1.0 > refcoord-scaling = com > energygrps = thin_film SOL > comm-mode= Linear > nstcomm = 100 > comm-grps= Thin_fiml SOL > %- > > Thank you > Alex > > On Tue, Apr 7, 2020 at 5:06 PM Justin Lemkul wrote: > >> >> >> On 4/7/20 5:00 PM, Alex wrote: >> > Dear all, >> > After minimization and equalizations using nvt (v-rescale) and npt (both >> > berendsen and ;Parrinello-Rahman), a simulation of mine could run well >> for >> > 200 ns using dt =0.001 while it would crash after 3 ns If I used dt = >> 0.002 >> > with the particles communication fatal error. >> > >> > Fatal error: >> > 2 particles communicated to PME rank 12 are more than 2/3 times the >> cut-off >> > out of the domain decomposition cell of their charge group in dimension >> y. >> > This usually means that your system is not well equilibrated. >> > >> > So, if the system would not be well equlibrated, then I would expect >> that >> > with dt = 0.001 the simulation wouldn't run well for 200 ns. But I >> expect >> > that it also crashes for example around 6 ns as the with the dt = 0.002 >> the >> > simulation last only 3 ns. >> > >> > Any comment that helps to understand the problem would be highly >> > appreciated. >> >> Please provide a description of what your system is and a full .mdp >> file. While most of the time these crashes come from poor equilibration, >> an inadequately parametrized topology or bad combination/misuse of >> algorithms can also cause crashes. >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalem...@vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> == >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- 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] Regarding version of gromacs
On 4/10/20 9:21 AM, FAISAL NABI wrote: I have tried the same few days back but it didn't work. I have been using gromacs 2018.1 earlier and then switched to 5.1.4 and it didn't work. Switching between major versions that are years apart in their development will not work, and GROMACS has never guaranteed backwards compatibility between major versions. Patch releases in the same release series (e.g. 5.1.4 vs 5.1.2) should be compatible because the .tpr version will not have changed, but one needs to question why move backwards and potentially introduce bugs that were fixed between versions? -Justin On Fri, Apr 10, 2020, 6:43 PM Ashma Khan wrote: Dear all, I have run my simulation on gromacs 5.1.4 for 200ns but now I want to extend my simulation to 500ns with gromacs 5.1.2. Is it possible or will there be problem during total simulation of 500ns in my systems. Please give me suggestion regarding this. -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh -- 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. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Converting a tpr file to an older version of gromacs
Hi Paul, Thank you for your reply. In fact, there is the GMXPBSA tool but I still have errors with that too when I run it on the examples provided in the installation folder. I tried to seek some help but the developers aren't responding. Thank you anyway! - Mariem Le ven. 10 avr. 2020 à 09:34, Paul bauer a écrit : > Hello, > > there is no real supported way of doing this. You would need to > re-create the TPR in the version you want to use it in. > Can you use an external tool instead of g_mmpbsa that supports reading > the newer file format? > > Cheers > > Paul > > On 09/04/2020 17:24, Mariem Ghoula wrote: > > Hi, > > > > I would like to use g_mmpbsa on my protein-protein complex simulation. > > However, after a few errors with the module due to tpr files version > > mismatch and after reading some posts with the same issue, I came to the > > conclusion that I need to convert my tpr file to an older version. Can > you > > please help me with this? After installing the old version of gromacs > that > > is compatible with the g_mmpbsa program, how can I convert my tpr file > > issued from an 2019.5 version to an older one (5.0.7)? > > > > Thanks a lot. > > > > - Mariem > > > -- > Paul Bauer, PhD > GROMACS Development Manager > KTH Stockholm, SciLifeLab > 0046737308594 > > -- > 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] dt in mdp
Thank you for the response. On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: > > > On 4/10/20 8:13 AM, Alex wrote: > > Dear Justin, > > Any comment please? > > Sorry, haven't had power/network for a while due to some bad storms here. > > GROMOS force fields are parametrized assuming all bonds are fixed, so > your constraints should be "all-bonds" not "h-bonds." > Interesting, hopefully that is the problem. > > I would also suggest you thoroughly validate the quality of the epoxy > molecule topology against QM data and bulk-phase properties, if possible. > As the ATB folks claim, the parameterization has been performed against a very high level DFT calculation, especially for the molecules with less than 50 atoms. I already have tested the density and it is in agreement with the experimental value. Regarding the "comm-grps = " , would you also please kindly let me know which one you would recommend for this system + plus a small single molecule called MOL_A which defuses from water inside the epoxy, specially for the PMF calculation of the Mol_A? comm-grps = Other SOL ;; (Other = thin_film and Mol_A) or comm-grps = system Thank you Alex > > -Justin > > > Regards, > > Alex > > > > On Tue, Apr 7, 2020 at 5:38 PM Alex wrote: > > > >> Thanks Justin for the response. > >> Please find below the mdp file. > >> The system is a thin film made out of a epoxy molecule, picture in be > >> below link, with water on top and bottom of the film. I even sometimes > have > >> the same issue when I simulate the bulk of this system, I mean a cubic > box > >> filled by this molecule and no water. > >> I got the force fields from the latest version of ATB repository by > which > >> I have previously done some other simulation for the same molecule. > >> > >> https://drive.google.com/open?id=1tJLxh9jQ2v5DDTrVR8IuQz40B3NN0zlb > >> > >> %mdp--- > >> title= Thin-Film > >> integrator = md > >> dt = 0.002 ; 2 fs ;0.001 1 fs > >> nsteps = 2500 ; 50 ns ;5000 ; 50 ns > >> xtc-precision= 500 ; 1000 > >> ;nstlist = 40 > >> %- > >> ;;in .trr file > >> nstxout = 3000 ; 6000 > >> nstvout = 0 > >> nstfout = 0 > >> ;;in energy file.log > >> nstlog = 2000 ; 4000 > >> nstcalcenergy= 2000 ;4000 > >> nstenergy= 2000 ;4000 > >> ;;in xtc file > >> nstxout-compressed = 0 > >> ;compressed-x-grps= non-Water > >> %- > >> continuation = yes > >> gen-vel = no > >> constraint-algorithm = lincs > >> constraints = h-bonds > >> cutoff-scheme= Verlet > >> coulombtype = PME > >> rcoulomb = 1.4 > >> > >> vdwtype = Cut-off > >> rvdw = 1.4 > >> DispCorr = EnerPres > >> > >> tcoupl= v-rescale > >> tc-grps = system > >> tau-t = 1.5 > >> nhchainlength = 10 > >> ref-t = 298.15 > >> pbc = xyz > >> > >> pcoupl = Parrinello-Rahman > >> Pcoupltype = isotropic > >> tau_p= 2.5 > >> compressibility = 4.5e-5 > >> ref_p= 1.0 > >> refcoord-scaling = com > >> energygrps = thin_film SOL > >> comm-mode= Linear > >> nstcomm = 100 > >> comm-grps= Thin_fiml SOL > >> %- > >> > >> Thank you > >> Alex > >> > >> On Tue, Apr 7, 2020 at 5:06 PM Justin Lemkul wrote: > >> > >>> > >>> On 4/7/20 5:00 PM, Alex wrote: > Dear all, > After minimization and equalizations using nvt (v-rescale) and npt > (both > berendsen and ;Parrinello-Rahman), a simulation of mine could run well > >>> for > 200 ns using dt =0.001 while it would crash after 3 ns If I used dt = > >>> 0.002 > with the particles communication fatal error. > > Fatal error: > 2 particles communicated to PME rank 12 are more than 2/3 times the > >>> cut-off > out of the domain decomposition cell of their charge group in > dimension > >>> y. > This usually means that your system is not well equilibrated. > > So, if the system would not be well equlibrated, then I would expect > >>> that > with dt = 0.001 the simulation wouldn't run well for 200 ns. But I > >>> expect > that it also crashes for example around 6 ns as the with the dt = > 0.002 > >>> the > simulation last only 3 ns. > > Any comment that helps to understand the problem would be highly > appreciated. > >>> Please provide a description of what your system is and a full .mdp > >>> file. While most of the time these crashes come from poor >
Re: [gmx-users] Regarding version of gromacs
I have tried the same few days back but it didn't work. I have been using gromacs 2018.1 earlier and then switched to 5.1.4 and it didn't work. On Fri, Apr 10, 2020, 6:43 PM Ashma Khan wrote: > Dear all, > I have run my simulation on gromacs 5.1.4 for 200ns but now I want to > extend my simulation to 500ns with gromacs 5.1.2. Is it possible or will > there be problem during total simulation of 500ns in my systems. Please > give me suggestion regarding this. > > -- > Ashma Khan > Research Scholar > Department of Chemistry > AMU, Aligarh > -- > 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] Regarding version of gromacs
Dear all, I have run my simulation on gromacs 5.1.4 for 200ns but now I want to extend my simulation to 500ns with gromacs 5.1.2. Is it possible or will there be problem during total simulation of 500ns in my systems. Please give me suggestion regarding this. -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh -- 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] Converting a tpr file to an older version of gromacs
Hello, there is no real supported way of doing this. You would need to re-create the TPR in the version you want to use it in. Can you use an external tool instead of g_mmpbsa that supports reading the newer file format? Cheers Paul On 09/04/2020 17:24, Mariem Ghoula wrote: Hi, I would like to use g_mmpbsa on my protein-protein complex simulation. However, after a few errors with the module due to tpr files version mismatch and after reading some posts with the same issue, I came to the conclusion that I need to convert my tpr file to an older version. Can you please help me with this? After installing the old version of gromacs that is compatible with the g_mmpbsa program, how can I convert my tpr file issued from an 2019.5 version to an older one (5.0.7)? Thanks a lot. - Mariem -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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] treating trajectory for diffusion calculations
Hi All, I have a coarse-grained simulation box with water and oil phases. Just playing with the diffusion 'only on a single particle' (single martini coarse bead) gave me different results when I use -rmcomm on trajectories with and without -pbc nojump. NOTE: selected only single bead Same diffusion results: gmx msd -s md.tpr -n index.ndx -f md.xtc # D=2.8914 x1e-5 cm^2/s gmx msd -s md.tpr -n index.ndx -f nojump.xtc # D=2.8914 x1e-5 cm^2/s Different diffusion results: gmx msd -s md.tpr -n index.ndx -f md.xtc -rmcomm #D= 2.491e-15 x 1e-5 cm^2/s gmx msd -s md.tpr -n index.ndx -f nojump.xtc -rmcomm #D = 7.03e-16 x1e-5 cm^2/s Also, I note that -rmcomm D values are very different (factor slow by e-15) from when I don't use rmcomm. What is the correct way to treat trajectory here before calculating msd? I have run my simulation as comm-grps whole system (default option). I am not sure when should I use -rmcomm option (in gmx msd) though the MSD numbers look more relevant if I don't use this. Thanks Dave -- 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] treating trajectory for diffusion calculations
Ah! am sorry, I figured out. Please ignore my mail. I was using wrong group selection for rmcomm in the command line. Sorry to all! Dave On Thu, Apr 9, 2020 at 11:26 PM Dave M wrote: > Hi All, > > I have a coarse-grained simulation box with water and oil phases. Just > playing with the diffusion 'only on a single particle' (single martini > coarse bead) gave me different results when I use -rmcomm on trajectories > with and without -pbc nojump. > > NOTE: selected only single bead > > Same diffusion results: > gmx msd -s md.tpr -n index.ndx -f md.xtc # D=2.8914 x1e-5 cm^2/s > gmx msd -s md.tpr -n index.ndx -f nojump.xtc # D=2.8914 x1e-5 cm^2/s > > Different diffusion results: > gmx msd -s md.tpr -n index.ndx -f md.xtc -rmcomm #D= 2.491e-15 x 1e-5 > cm^2/s > gmx msd -s md.tpr -n index.ndx -f nojump.xtc -rmcomm #D = 7.03e-16 x1e-5 > cm^2/s > > Also, I note that -rmcomm D values are very different (factor slow by > e-15) from when I don't use rmcomm. What is the correct way to treat > trajectory here before calculating msd? I have run my simulation as > comm-grps whole system (default option). I am not sure when should I use > -rmcomm option (in gmx msd) though the MSD numbers look more relevant if I > don't use this. > > Thanks > Dave > -- 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] Buggy 2020?
Hello All, I am wondering if gromacs-2020 is buggy? or I am missing something?. In gromacs-2020, for a certain setup, I got following warning, WARNING: There are no atom pairs for dispersion correction But, for same system, gromacs-2019 does not give warning. Apparently, gromacs-2020 gives zero in dispersion correction, whereas gormacs-2019 gives non-zero dispersion correction. Regards, Masrul -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fwd: Fwd: geometry optimization of metalloenzyme
Thank you, Justin. I am still struggling with constraints. I am trying to use "*freezegrps*" and "*freezedim*" to run an NVT equilibration of a structure (successfully geometry-optimized using freezegrps). However, when I try to build the binary using my optimized structure, I get either "Segmentation fault" or the following error: "free(): invalid next size (fast) Aborted" These messages seem to indicate a memory allocation problem, but I cannot isolate the problem. I am not sure of the correct combination of constraint (lincs) keywords in the nvt input, especially how to combine these with the freezegrps/freezedim commands. Do anybody have any tips or helpful examples? On Thu, Apr 2, 2020 at 9:26 PM Justin Lemkul wrote: > > > On 4/2/20 3:23 PM, Nadia Elghobashi-Meinhardt wrote: > > Hello everyone, > > > > I am trying to minimize the potential energy of a > > metalloenzyme containing Ni and Fe atoms. > > What is the best way to constrain (fix?) the position of the active site > > atoms > > during the geometry optimization? > > I have tried introducing bonds with relatively high force constants and > > alternatively, tried introducing a [constraints] section, > > but the atoms are still not staying put. > > Bonds or constraints will maintain distances between atoms (relative > position) but not absolute position. > > > Or should one use extra position restraints? > > If the absolute position matters, yes. I would think the approach of > adding restraints or constraints between atoms would be more meaningful > given that preserving coordination geometry is often the defect in MM > treatment of transition metals. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 pdb2gmx
On 4/10/20 12:15 PM, Elham Taghikhani wrote: Hi I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. In the topology, I got this warning message : Warning:long-bond... I don't know what should I do to retain the covalent bond. I will appreciate it if you help me with this problem. The full screen output of pdb2gmx would be informative here. If the long bond occurs between the residues flanking your modified residue, you forgot step 5 in http://manual.gromacs.org/documentation/current/how-to/topology.html#adding-a-new-residue If that doesn't solve it, please post the full screen output from pdb2gmx. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem with pdb2gmx
Hi I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format. In the topology, I got this warning message : Warning:long-bond... I don't know what should I do to retain the covalent bond. I will appreciate it if you help me with this problem. -- 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 version issue
Dear GROMACS developers, I am performing classical MD simulations of a membrane protein system, using GROMACS 2018.6 version. I have just noticed that after few nano seconds, the box dimensions are changing. Meaning that the system shrinks along the z-axis, for example dimensions are changing from 98.4 x 98.4 x 299.1 (A^3) to 116.8 x 116.8 x 212.9 (A^3). After trying so many possibilities, I've realised it is a version specific problem. Trying GROMACS 2019.4 the problem is totally solved. I was wondering if you could explain the reason. Thank you in advance. Best regards, Yasaman -- 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 version issue
On 4/10/20 11:04 AM, Yasaman KARAMI wrote: Dear GROMACS developers, I am performing classical MD simulations of a membrane protein system, using GROMACS 2018.6 version. I have just noticed that after few nano seconds, the box dimensions are changing. Meaning that the system shrinks along the z-axis, for example dimensions are changing from 98.4 x 98.4 x 299.1 (A^3) to 116.8 x 116.8 x 212.9 (A^3). After trying so many possibilities, I've realised it is a version specific problem. Trying GROMACS 2019.4 the problem is totally solved. I was wondering if you could explain the reason. If you're using the CHARMM force field, this was an issue related to incorrect treatment of CMAP terms when the protein crossed a periodic boundary. The issue was recently solved so you should use the newer GROMACS version. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] segmentation fault gmx do_dssp
Hello, I guess the problem is about memory. You could strip the water and ions first, then process the striped trajectory. All the best, Qinghua On 4/10/20 11:48 PM, Sadaf Rani wrote: Dear Gromacs users I am doing an analysis of protein-ligand MD simulation of 150ns. I am trying to calculate secondary structure as below:- gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1 But I am getting segmentation fault error. Reading file md.tpr, VERSION 2020-UNCHECKED (single precision) Reading file md.tpr, VERSION 2020-UNCHECKED (single precision) Not all residues were recognized (489 from 40652), the result may be inaccurate! Group 0 ( System) has 128526 elements Group 1 (Protein) has 7893 elements Group 2 ( Protein-H) has 3971 elements Group 3 (C-alpha) has 489 elements Group 4 ( Backbone) has 1467 elements Group 5 ( MainChain) has 1957 elements Group 6 ( MainChain+Cb) has 2415 elements Group 7 (MainChain+H) has 2424 elements Group 8 ( SideChain) has 5469 elements Group 9 (SideChain-H) has 2014 elements Group10 (Prot-Masses) has 7893 elements Group11 (non-Protein) has 120633 elements Group12 ( Other) has 173 elements Group13 (G6P) has27 elements Group14 (NAP) has73 elements Group15 (NAS) has73 elements Group16 ( NA) has10 elements Group17 ( Water) has 120450 elements Group18 (SOL) has 120450 elements Group19 ( non-Water) has 8076 elements Group20 (Ion) has10 elements Group21 (G6P) has27 elements Group22 (NAP) has73 elements Group23 (NAS) has73 elements Group24 ( NA) has10 elements Group25 ( Water_and_ions) has 120460 elements Select a group: 5 Selected 5: 'MainChain' There are 489 residues in your selected group dssp cmd='/usr/local/bin/dssp -i ddvbUtB6 2>/dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddvbUtB6 to ./#ddvbUtB6.1# Segmentation fault (core dumped) How should I fix it. As my system is protein-ligand should I choose a group having protein and ligand together for this analysis? Any suggestions will really help. Thanks. Sadaf -- 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] dt in mdp
On 4/10/20 4:17 PM, Alex wrote: On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul wrote: On 4/10/20 9:16 AM, Alex wrote: Thank you for the response. On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: On 4/10/20 8:13 AM, Alex wrote: Dear Justin, Any comment please? Sorry, haven't had power/network for a while due to some bad storms here. GROMOS force fields are parametrized assuming all bonds are fixed, so your constraints should be "all-bonds" not "h-bonds." Interesting, hopefully that is the problem. By constraining all the bonds "constraints = all-bonds", the simulation crashes in the first step immediately irrespective to the starting point of simulation, even if I continue the old working simulation. Now we're getting somewhere. That suggests that at least one bond has deviated substantially from its equilibrium length, such that the constraint algorithm fails immediately. This also likely underlies the original failure - forces are building up on some atoms such that mdrun crashes. You have either a bad geometry, inadequate topology, or both. Inspect the molecule(s) that mdrun complains about to see if the molecules are distorted by computing bond lengths and comparing against the force field's parameters. It may be beneficial to re-minimize and equilibrate with the proper constraint scheme after validating that the topology is of sufficient quality. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] segmentation fault gmx do_dssp
Dear Gromacs users I am doing an analysis of protein-ligand MD simulation of 150ns. I am trying to calculate secondary structure as below:- gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1 But I am getting segmentation fault error. Reading file md.tpr, VERSION 2020-UNCHECKED (single precision) Reading file md.tpr, VERSION 2020-UNCHECKED (single precision) Not all residues were recognized (489 from 40652), the result may be inaccurate! Group 0 ( System) has 128526 elements Group 1 (Protein) has 7893 elements Group 2 ( Protein-H) has 3971 elements Group 3 (C-alpha) has 489 elements Group 4 ( Backbone) has 1467 elements Group 5 ( MainChain) has 1957 elements Group 6 ( MainChain+Cb) has 2415 elements Group 7 (MainChain+H) has 2424 elements Group 8 ( SideChain) has 5469 elements Group 9 (SideChain-H) has 2014 elements Group10 (Prot-Masses) has 7893 elements Group11 (non-Protein) has 120633 elements Group12 ( Other) has 173 elements Group13 (G6P) has27 elements Group14 (NAP) has73 elements Group15 (NAS) has73 elements Group16 ( NA) has10 elements Group17 ( Water) has 120450 elements Group18 (SOL) has 120450 elements Group19 ( non-Water) has 8076 elements Group20 (Ion) has10 elements Group21 (G6P) has27 elements Group22 (NAP) has73 elements Group23 (NAS) has73 elements Group24 ( NA) has10 elements Group25 ( Water_and_ions) has 120460 elements Select a group: 5 Selected 5: 'MainChain' There are 489 residues in your selected group dssp cmd='/usr/local/bin/dssp -i ddvbUtB6 2>/dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddvbUtB6 to ./#ddvbUtB6.1# Segmentation fault (core dumped) How should I fix it. As my system is protein-ligand should I choose a group having protein and ligand together for this analysis? Any suggestions will really help. Thanks. Sadaf -- 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] segmentation fault gmx do_dssp
On 4/10/20 5:48 PM, Sadaf Rani wrote: Dear Gromacs users I am doing an analysis of protein-ligand MD simulation of 150ns. I am trying to calculate secondary structure as below:- gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1 But I am getting segmentation fault error. Reading file md.tpr, VERSION 2020-UNCHECKED (single precision) Reading file md.tpr, VERSION 2020-UNCHECKED (single precision) Not all residues were recognized (489 from 40652), the result may be inaccurate! Group 0 ( System) has 128526 elements Group 1 (Protein) has 7893 elements Group 2 ( Protein-H) has 3971 elements Group 3 (C-alpha) has 489 elements Group 4 ( Backbone) has 1467 elements Group 5 ( MainChain) has 1957 elements Group 6 ( MainChain+Cb) has 2415 elements Group 7 (MainChain+H) has 2424 elements Group 8 ( SideChain) has 5469 elements Group 9 (SideChain-H) has 2014 elements Group10 (Prot-Masses) has 7893 elements Group11 (non-Protein) has 120633 elements Group12 ( Other) has 173 elements Group13 (G6P) has27 elements Group14 (NAP) has73 elements Group15 (NAS) has73 elements Group16 ( NA) has10 elements Group17 ( Water) has 120450 elements Group18 (SOL) has 120450 elements Group19 ( non-Water) has 8076 elements Group20 (Ion) has10 elements Group21 (G6P) has27 elements Group22 (NAP) has73 elements Group23 (NAS) has73 elements Group24 ( NA) has10 elements Group25 ( Water_and_ions) has 120460 elements Select a group: 5 Selected 5: 'MainChain' There are 489 residues in your selected group dssp cmd='/usr/local/bin/dssp -i ddvbUtB6 2>/dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddvbUtB6 to ./#ddvbUtB6.1# Segmentation fault (core dumped) How should I fix it. As my system is protein-ligand should I choose a group having protein and ligand together for this analysis? The selection does not depend on the contents of the system; either MainChain or MainChain+H should work. You need to verify that your dssp binary works correctly and that its version matches what is expected by GROMACS. You may need to use the -ver option. See the many posts on this very topic in the archive. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Protonated ligand free energy calculation in water
Dear GROMACS users, I read and followed Dr. Lemkul's tutorial on Free Energy Calculation on the webpage, http://www.mdtutorials.com/gmx/free_energy/index.html It is very helpful and easy to follow, but my ligand is protonated so the atomic charges in the topol.top are non-zero. The above tutorial also indicates that Coulombic interactions can be applied, but I would like to know how it can be done? vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00 coul_lambdas= 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00 Here is the [ atoms ] in my topol.top and your advise is highly appreciated! [ atoms ] ; nr type resnr residue atom cgnrcharge mass typeB chargeB massB ; residue1 MT3 rtp MT3 q 2.0 1 nh 1MT3 N1 1 -0.83505600 14.01 ; qtot -0.835056 2 cz 1MT3 C1 2 0.85138300 12.01 ; qtot 0.016327 3 nh 1MT3 N2 3 -0.51848300 14.01 ; qtot -0.502156 4 nh 1MT3 N3 4 -0.83505600 14.01 ; qtot -1.337212 5 c3 1MT3 C2 5 -0.34660600 12.01 ; qtot -1.683818 6 nh 1MT3 N4 6 0.02468700 14.01 ; qtot -1.659131 7 nh 1MT3 N5 7 -0.80566500 14.01 ; qtot -2.464796 8 cz 1MT3 C3 8 0.57808800 12.01 ; qtot -1.886708 9 c3 1MT3 C4 9 -0.34660600 12.01 ; qtot -2.233314 10 hn 1MT3 H1 10 0.47045200 1.008000 ; qtot -1.762862 11 hn 1MT3 H2 11 0.47045200 1.008000 ; qtot -1.292410 12 hn 1MT3 H3 12 0.38772400 1.008000 ; qtot -0.904686 13 hn 1MT3 H4 13 0.47045200 1.008000 ; qtot -0.434234 14 h1 1MT3 H5 14 0.17432200 1.008000 ; qtot -0.259912 15 h1 1MT3 H6 15 0.17432200 1.008000 ; qtot -0.085590 16 h1 1MT3 H7 16 0.17432200 1.008000 ; qtot 0.088732 17 hn 1MT3 H8 17 0.45892600 1.008000 ; qtot 0.547658 18 h1 1MT3 H9 18 0.17432200 1.008000 ; qtot 0.721980 19 h1 1MT3H10 19 0.17432200 1.008000 ; qtot 0.896302 20 h1 1MT3H11 20 0.17432200 1.008000 ; qtot 1.070624 21 hn 1MT3H12 21 0.45892600 1.008000 ; qtot 1.529550 22 hn 1MT3H13 22 0.47045200 1.008000 ; qtot 2.02 Thank you, Rolly -- 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] dt in mdp
On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul wrote: > > > On 4/10/20 9:16 AM, Alex wrote: > > Thank you for the response. > > > > > > On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote: > > > >> > >> On 4/10/20 8:13 AM, Alex wrote: > >>> Dear Justin, > >>> Any comment please? > >> Sorry, haven't had power/network for a while due to some bad storms > here. > >> > >> GROMOS force fields are parametrized assuming all bonds are fixed, so > >> your constraints should be "all-bonds" not "h-bonds." > >> > > Interesting, hopefully that is the problem. > By constraining all the bonds "constraints = all-bonds", the simulation crashes in the first step immediately irrespective to the starting point of simulation, even if I continue the old working simulation. Regards, Alex > > > > > >> I would also suggest you thoroughly validate the quality of the epoxy > >> molecule topology against QM data and bulk-phase properties, if > possible. > >> > > As the ATB folks claim, the parameterization has been performed against a > > very high level DFT calculation, especially for the molecules with less > > than 50 atoms. > > I already have tested the density and it is in agreement with the > > experimental value. > > > > Regarding the "comm-grps = " , would you also please kindly let me know > > which one you would recommend for this system + plus a small single > > molecule called MOL_A which defuses from water inside the epoxy, > specially > > for the PMF calculation of the Mol_A? > > comm-grps = Other SOL ;; (Other = thin_film and Mol_A) > > or > > comm-grps = system > > I saw the conversation with David about this. I have nothing to add that > he hasn't already said. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to extend the force field by polariation parameters
Dear Justin, thank you for your answer. As I noticed, there is a model of Drude oscillators (shells) used in GROMACS to represent the polarization of atoms. However, there exists model of rigid rod dipole moment which, instead of oscillating distance between the core nucleus and the auxiliary particle, assumes rigid length between them. In this model, the virtual site has no van der Waals interactions, while it has a charge q and a mass m. Unlike the Drude oscillator, this rod a has a finite dipole moment = charge x length. Thus, it requires an orientational averaging (i.e., T > 0) to produce physically meaningful results. The rod involves three parameters: length, charge, and mass.The polarizability is (charge x length)^2/(3kbT) and the intrinsic time scale is given by (2kbT/(length^2 x mass)^0.5. Such a model has been already used. The authors carried out the simulations for graphene (GRAPPA FF) using GROMACS (Nanoscale, 2014, 6, 5438). I just wonder if I could adopt this model without changes in code by using virtual interaction sites. Thanks. Greetings Zuzana - Original Message - From: "Justin Lemkul" To: "gmx-users" Sent: Friday, April 10, 2020 3:05:47 PM Subject: Re: [gmx-users] How to extend the force field by polariation parameters On 4/9/20 8:06 PM, Zuzana Benkova wrote: > Dear GROMACS users, > > I am trying to extend the CHARMM force field of graphene by polarization of > carbon atoms. I need to use the rigid rod dipole model, with a dipole on each > carbon atom, with length of 0.7 A° combined with a charge of 0.1 e, which > yields a polarization of 0.910 A°^3 (GRAPPA). > > Can you suggest me some literature where I can get some idea how to do it? In > GROMACS manual, I have found Chapter 4.4. related to the polarization but it > contains only information on simple polarization, water polarization and > Thole polarization and doesn't provide some hint how to extend a given force > field. If your model has a fixed length between the core nucleus and the auxiliary particle, it's not a "polarizable" model because the dipoles cannot relax/change length, therefore nothing related to polarization options is relevant to you. You will have particles that are at a fixed distance from their nucleus (e.g. via [constraints]) -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] energy minimizing
hi friends I generated a box of mixed gas with gmx insert-moleculesI ran an energy minimizing. the potential energy is 4.05e+07 and maximum force is 1.25e+03.I used different algorithm likes cg and steep for minimization. what do I have to do untill my system potential energy has negative value??I need a information about energy minimizing and potential energy. I know that positive value of potential energy means the intermolecular interaction is weaker than intramolecular interaction but I don't know how I can control this matter. please help Sent from Yahoo Mail on Android -- 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] segmentation fault gmx do_dssp
Dear Justin and Qinghua I am using gromacs 2020 for analysis and dssp version on my system is 2.2.1. Which version of dssp would be compatible with gromacs 2020? Qinghua, I am already using the stripped trajectory. Any suggestions would be appreciated. Thanks. Sadaf -- 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] segmentation fault gmx do_dssp
On 4/10/20 8:07 PM, Sadaf Rani wrote: Dear Justin and Qinghua I am using gromacs 2020 for analysis and dssp version on my system is 2.2.1. Which version of dssp would be compatible with gromacs 2020? Your version should be fine, but make sure the dssp binary works properly on its own (not via do_dssp) and try specifying -ver 2 when running do_dssp. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx: Selecting Force Field in first command
On 4/10/20 9:03 PM, ferna...@hypernetlabs.io wrote: Hi all! Context I'm trying to run simple gromacs example commands below * gmx pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce * gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc In a Docker container with a Dockerfile (Dockerfile = instruction file for auto execution inside the container) containing the below: FROM mariojmdavid/gromacs-cuda:2019.3-runtime <-- thanks Mario! :) WORKDIR /usr/local/gromacs COPY . /usr/local/gromacs ENTRYPOINT ["/usr/local/gromacs/bin/gmx","pdb2gmx", "-f", "1aki.pdb", "-o", "1aki_processed.gro", "-water", "spce"] Problem Both simple examples ask to 'Select the Force Field' after the 1st command is executed. A Docker container is non-interactive so I can't really pass my option for Force Field after I send it off to auto-execute remotely. Question Does anyone know how I can pass my Force Field selection from the start? That's what the -ff flag does. See gmx help pdb2gmx for all command-line options. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding version of gromacs
Thank you Justin for your suggestion As I run my simulation on supercomputer and there is availability of gromacs-5.1.2 version not 5.1.4. Earlier it had 5.1.4 version but now it has only 5.1.2 version. -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh -- 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] Regarding version of gromacs
On 4/10/20 9:20 PM, Ashma Khan wrote: Thank you Justin for your suggestion As I run my simulation on supercomputer and there is availability of gromacs-5.1.2 version not 5.1.4. Earlier it had 5.1.4 version but now it has only 5.1.2 version. You can always install the version you want in your home directory. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to extend the force field by polariation parameters
On 4/10/20 6:44 PM, Zuzana Benkova wrote: Dear Justin, thank you for your answer. As I noticed, there is a model of Drude oscillators (shells) used in GROMACS to represent the polarization of atoms. However, there exists model of rigid rod dipole moment which, instead of oscillating distance between the core nucleus and the auxiliary particle, assumes rigid length between them. In this model, the virtual site has no van der Waals interactions, while it has a charge q and a mass m. Unlike the Drude oscillator, this rod a has a finite dipole moment = charge x length. Thus, it requires an orientational averaging (i.e., T > 0) to produce physically meaningful results. The rod involves three parameters: length, charge, and mass.The polarizability is (charge x length)^2/(3kbT) and the intrinsic time scale is given by (2kbT/(length^2 x mass)^0.5. Such a model has been already used. The authors carried out the simulations for graphene (GRAPPA FF) using GROMACS (Nanoscale, 2014, 6, 5438). I just wonder if I could adopt this model without changes in code by using virtual interaction sites. No, Drude oscillators are not virtual sites, but you also do not need any code changes, either. If the study was published using GROMACS, you should contact the authors and ask for sample inputs. But it should be rather simple to set this up. I would argue this is not really a Drude model because the atom-"Drude" length is fixed. While the dipole can reorient, it cannot, by definition, oscillate if the length is constrained. All you have are additional atoms. They carry charge, have mass, and exist at fixed length from their parent atoms, which can be accomplished with [constraints] for all the dipoles. -Justin Thanks. Greetings Zuzana - Original Message - From: "Justin Lemkul" To: "gmx-users" Sent: Friday, April 10, 2020 3:05:47 PM Subject: Re: [gmx-users] How to extend the force field by polariation parameters On 4/9/20 8:06 PM, Zuzana Benkova wrote: Dear GROMACS users, I am trying to extend the CHARMM force field of graphene by polarization of carbon atoms. I need to use the rigid rod dipole model, with a dipole on each carbon atom, with length of 0.7 A° combined with a charge of 0.1 e, which yields a polarization of 0.910 A°^3 (GRAPPA). Can you suggest me some literature where I can get some idea how to do it? In GROMACS manual, I have found Chapter 4.4. related to the polarization but it contains only information on simple polarization, water polarization and Thole polarization and doesn't provide some hint how to extend a given force field. If your model has a fixed length between the core nucleus and the auxiliary particle, it's not a "polarizable" model because the dipoles cannot relax/change length, therefore nothing related to polarization options is relevant to you. You will have particles that are at a fixed distance from their nucleus (e.g. via [constraints]) -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pdb2gmx: Selecting Force Field in first command
Hi all! Context I'm trying to run simple gromacs example commands below * gmx pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce * gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc In a Docker container with a Dockerfile (Dockerfile = instruction file for auto execution inside the container) containing the below: FROM mariojmdavid/gromacs-cuda:2019.3-runtime <-- thanks Mario! :) WORKDIR /usr/local/gromacs COPY . /usr/local/gromacs ENTRYPOINT ["/usr/local/gromacs/bin/gmx","pdb2gmx", "-f", "1aki.pdb", "-o", "1aki_processed.gro", "-water", "spce"] Problem Both simple examples ask to 'Select the Force Field' after the 1st command is executed. A Docker container is non-interactive so I can't really pass my option for Force Field after I send it off to auto-execute remotely. Question Does anyone know how I can pass my Force Field selection from the start? Many thanks in advance! Fernando -- 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] Buggy 2020?
Hi, Based on what is in your system, what do you think the behavior should be? A change reflects that one of the versions may be wrong, but not that the new one is necessarily it. Mark On Fri, 10 Apr 2020 at 08:17, Parvez Mh wrote: > Hello All, > > I am wondering if gromacs-2020 is buggy? or I am missing something?. In > gromacs-2020, for a certain setup, I got following warning, > WARNING: There are no atom pairs for dispersion correction > > But, for same system, gromacs-2019 does not give warning. Apparently, > gromacs-2020 gives zero in dispersion correction, whereas > gormacs-2019 gives non-zero dispersion correction. > > Regards, > Masrul > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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.
