Re: [gmx-users] Fat-bottom restrain
Hi Mark, I am using Gromacs v.2018.x and as I tested it is not the matter of using GPU or CPU. The issue was from my side where by mistake I had put the wall (in all posre.x,y,z.itp) exactly on the outer box borders so that my inner box and outer box were fully identical, so the molecules had no limitation and wherever of the simulation box they could go, that is why the gmx energy shows the "Flat-bottom posres" portion but it was absolutely zero. However, my question now is; do I have flat-bottom restrains in these simulation or not? e.g. If I want to report these simulations somewhere should I mention that I have used (I haven't used) flat-bottom restrains in these simulation? Thank you Alex On Wed, Sep 11, 2019 at 8:01 PM Mark Abraham wrote: > Hi, > > It's certainly conceivable that such restraints are ineffective in some run > modes. However, "on the GPU" describes a range of scenarios. If you're > running with 2019.x, does adding -bonded cpu to the mdrun command line > restore the functionality? > > Otherwise, please try the "working CPU" run on a GPU resource and vice > versa to see what we learn. > > Mark > > On Wed, 11 Sep 2019 at 23:21, Alex wrote: > > > Thanks Billy, > > > > > If the flat bottom restraint energy is zero, then that means that the > > > restraints aren't being applied, or your predefined distance is not > being > > > exceeded. I doubt you would get binary zero values if it was the > second > > > option, so something is probably wrong with your syntax or your > inclusion > > > of the restraints > > > > As far as I have inspected everything is fine with the syntax and > > application of the restraints. Using similar way works fine in another > > system. The only difference is that one (not working one) runs on GPU and > > the other one (the working one) runs on CPU, and I am not sure if that > > plays any role and if the flat-bottom restrain doesn't work on GPU! > > > > > > > > Cheers, > > > Billy > > > > > > On Wed., 11 Sep. 2019, 5:20 pm Billy Williams-Noonan, < > > > billy.williams-noo...@monash.edu> wrote: > > > > > > You may want to consider using smart-bottom restraints instead? > > I haven't hear the smart-bottom one, would you please explain more? or > > address me to a reference? > > > > > > Jokes aside, why does it matter if your molecules move into the next > > > periodic image? > > Just to avoid percolation across the period box. > > > > > > Cheers, > > > Billy > > Thank you, > > Alex > > > > On Wed, Sep 11, 2019 at 3:02 AM Alex wrote: > > > > > Hi, > > > > > > Any comment, please? > > > > > > Thank you. > > > Alex > > > > > > On Mon, Sep 9, 2019 at 10:22 PM Alex > wrote: > > > > > >> Hi Mark, > > >> > > >> Thank you for your response. > > >> Here are the part of options that gmx energy gives me out: > > >> > > >> 9 Coulomb-(SR)10 Coul.-recip. > > >> 11 Flat-bottom-posres 12 Potential > > >> 13 Kinetic-En. 14 Total-Energy15 Conserved-En > > >> > > >> > > >> Energy Average Err.Est. RMSD Tot-Drift > > >> > > >> > > > --- > > >> Coulomb (SR) -8.4629e+061505041.75 -840.379 > > >> (kJ/mol) > > >> Coul. recip.12689.7 12109.811 -83.8453 > > >> (kJ/mol) > > >> Flat-bottom posres0 0 0 0 > > >> (kJ/mol) > > >> Potential-7.29781e+065403208.53 -3702.71 > > >> (kJ/mol) > > >> Kinetic En. 1.20527e+068.21912.61-12.144 > > >> (kJ/mol) > > >> Total Energy -6.09255e+06540 3942.5 -3714.84 > > >> (kJ/mol) > > >> Conserved En.-2.97263e+06 89 1.81911e+06 > 6.30101e+06 > > >> (kJ/mol) > > >> > > >> As can be seen above the Flat-bottom posres energy is just zero during > > >> the simulation; and even stiffening the force constant from 4184 > > KJ/(mol. > > >> nm^2) to 4184000 KJ/(mol. nm^2) doesn't change anythings and the > > >> Flat-bottom posres energy would remain absolutely zero! > > >> > > >> I rechecked everything and I don't see any problem with the way I have > > >> set the flat-bottom restrain. > > >> Any comment would be highly appreciated. > > >> > > >> Thank you, > > >> Alex > > >> > > >> > > >> > > >> On Sat, Sep 7, 2019 at 10:47 AM Mark Abraham < > mark.j.abra...@gmail.com> > > >> wrote: > > >> > > >>> Hi, > > >>> > > >>> The total potential energy violating the restraints is reported, so > you > > >>> should see that there is an appropriate contribution there, and > > probably > > >>> plan to stiffen the force constant. > > >>> > > >>> Mark > > >>> > > >>> On Fri., 6 Sep. 2019, 17:23 Alex, wrote: > > >>> > > >>> > Dear all, > > >>> > Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to > > have > > >>> a > > >>> > smaller cubic box as semi-preamble walls inside a bigger cubic box > so > >
Re: [gmx-users] Fat-bottom restrain
Hi, It's certainly conceivable that such restraints are ineffective in some run modes. However, "on the GPU" describes a range of scenarios. If you're running with 2019.x, does adding -bonded cpu to the mdrun command line restore the functionality? Otherwise, please try the "working CPU" run on a GPU resource and vice versa to see what we learn. Mark On Wed, 11 Sep 2019 at 23:21, Alex wrote: > Thanks Billy, > > > If the flat bottom restraint energy is zero, then that means that the > > restraints aren't being applied, or your predefined distance is not being > > exceeded. I doubt you would get binary zero values if it was the second > > option, so something is probably wrong with your syntax or your inclusion > > of the restraints > > As far as I have inspected everything is fine with the syntax and > application of the restraints. Using similar way works fine in another > system. The only difference is that one (not working one) runs on GPU and > the other one (the working one) runs on CPU, and I am not sure if that > plays any role and if the flat-bottom restrain doesn't work on GPU! > > > > > Cheers, > > Billy > > > > On Wed., 11 Sep. 2019, 5:20 pm Billy Williams-Noonan, < > > billy.williams-noo...@monash.edu> wrote: > > > > You may want to consider using smart-bottom restraints instead? > I haven't hear the smart-bottom one, would you please explain more? or > address me to a reference? > > > > Jokes aside, why does it matter if your molecules move into the next > > periodic image? > Just to avoid percolation across the period box. > > > > Cheers, > > Billy > Thank you, > Alex > > On Wed, Sep 11, 2019 at 3:02 AM Alex wrote: > > > Hi, > > > > Any comment, please? > > > > Thank you. > > Alex > > > > On Mon, Sep 9, 2019 at 10:22 PM Alex wrote: > > > >> Hi Mark, > >> > >> Thank you for your response. > >> Here are the part of options that gmx energy gives me out: > >> > >> 9 Coulomb-(SR)10 Coul.-recip. > >> 11 Flat-bottom-posres 12 Potential > >> 13 Kinetic-En. 14 Total-Energy15 Conserved-En > >> > >> > >> Energy Average Err.Est. RMSD Tot-Drift > >> > >> > --- > >> Coulomb (SR) -8.4629e+061505041.75 -840.379 > >> (kJ/mol) > >> Coul. recip.12689.7 12109.811 -83.8453 > >> (kJ/mol) > >> Flat-bottom posres0 0 0 0 > >> (kJ/mol) > >> Potential-7.29781e+065403208.53 -3702.71 > >> (kJ/mol) > >> Kinetic En. 1.20527e+068.21912.61-12.144 > >> (kJ/mol) > >> Total Energy -6.09255e+06540 3942.5 -3714.84 > >> (kJ/mol) > >> Conserved En.-2.97263e+06 89 1.81911e+06 6.30101e+06 > >> (kJ/mol) > >> > >> As can be seen above the Flat-bottom posres energy is just zero during > >> the simulation; and even stiffening the force constant from 4184 > KJ/(mol. > >> nm^2) to 4184000 KJ/(mol. nm^2) doesn't change anythings and the > >> Flat-bottom posres energy would remain absolutely zero! > >> > >> I rechecked everything and I don't see any problem with the way I have > >> set the flat-bottom restrain. > >> Any comment would be highly appreciated. > >> > >> Thank you, > >> Alex > >> > >> > >> > >> On Sat, Sep 7, 2019 at 10:47 AM Mark Abraham > >> wrote: > >> > >>> Hi, > >>> > >>> The total potential energy violating the restraints is reported, so you > >>> should see that there is an appropriate contribution there, and > probably > >>> plan to stiffen the force constant. > >>> > >>> Mark > >>> > >>> On Fri., 6 Sep. 2019, 17:23 Alex, wrote: > >>> > >>> > Dear all, > >>> > Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to > have > >>> a > >>> > smaller cubic box as semi-preamble walls inside a bigger cubic box so > >>> that > >>> > all molecules except water would stay inside the smaller box during > the > >>> > simulation, however, the wall doesn't work and the molecules are also > >>> out > >>> > of the smaller box in several replica's simulations each with 100 ns. > >>> > The only reason I can imagine is that the K=4184 KJ/(mol. nm^2 is > >>> probably > >>> > too low to keep the molecules inside the smaller box! I wonder if you > >>> know > >>> > any other potential reason? how can I find out the reason? > >>> > > >>> > Regards, > >>> > Alex > >>> > P.S. I am sure that I am using the flat-bottom restrain correctly as > >>> the > >>> > same approach worked for some other systems of mine previously. > >>> > -- > >>> > 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 > >>> >
Re: [gmx-users] Fat-bottom restrain
Thanks Billy, > If the flat bottom restraint energy is zero, then that means that the > restraints aren't being applied, or your predefined distance is not being > exceeded. I doubt you would get binary zero values if it was the second > option, so something is probably wrong with your syntax or your inclusion > of the restraints As far as I have inspected everything is fine with the syntax and application of the restraints. Using similar way works fine in another system. The only difference is that one (not working one) runs on GPU and the other one (the working one) runs on CPU, and I am not sure if that plays any role and if the flat-bottom restrain doesn't work on GPU! > > Cheers, > Billy > > On Wed., 11 Sep. 2019, 5:20 pm Billy Williams-Noonan, < > billy.williams-noo...@monash.edu> wrote: > > You may want to consider using smart-bottom restraints instead? I haven't hear the smart-bottom one, would you please explain more? or address me to a reference? > > Jokes aside, why does it matter if your molecules move into the next > periodic image? Just to avoid percolation across the period box. > > Cheers, > Billy Thank you, Alex On Wed, Sep 11, 2019 at 3:02 AM Alex wrote: > Hi, > > Any comment, please? > > Thank you. > Alex > > On Mon, Sep 9, 2019 at 10:22 PM Alex wrote: > >> Hi Mark, >> >> Thank you for your response. >> Here are the part of options that gmx energy gives me out: >> >> 9 Coulomb-(SR)10 Coul.-recip. >> 11 Flat-bottom-posres 12 Potential >> 13 Kinetic-En. 14 Total-Energy15 Conserved-En >> >> >> Energy Average Err.Est. RMSD Tot-Drift >> >> --- >> Coulomb (SR) -8.4629e+061505041.75 -840.379 >> (kJ/mol) >> Coul. recip.12689.7 12109.811 -83.8453 >> (kJ/mol) >> Flat-bottom posres0 0 0 0 >> (kJ/mol) >> Potential-7.29781e+065403208.53 -3702.71 >> (kJ/mol) >> Kinetic En. 1.20527e+068.21912.61-12.144 >> (kJ/mol) >> Total Energy -6.09255e+06540 3942.5 -3714.84 >> (kJ/mol) >> Conserved En.-2.97263e+06 89 1.81911e+06 6.30101e+06 >> (kJ/mol) >> >> As can be seen above the Flat-bottom posres energy is just zero during >> the simulation; and even stiffening the force constant from 4184 KJ/(mol. >> nm^2) to 4184000 KJ/(mol. nm^2) doesn't change anythings and the >> Flat-bottom posres energy would remain absolutely zero! >> >> I rechecked everything and I don't see any problem with the way I have >> set the flat-bottom restrain. >> Any comment would be highly appreciated. >> >> Thank you, >> Alex >> >> >> >> On Sat, Sep 7, 2019 at 10:47 AM Mark Abraham >> wrote: >> >>> Hi, >>> >>> The total potential energy violating the restraints is reported, so you >>> should see that there is an appropriate contribution there, and probably >>> plan to stiffen the force constant. >>> >>> Mark >>> >>> On Fri., 6 Sep. 2019, 17:23 Alex, wrote: >>> >>> > Dear all, >>> > Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to have >>> a >>> > smaller cubic box as semi-preamble walls inside a bigger cubic box so >>> that >>> > all molecules except water would stay inside the smaller box during the >>> > simulation, however, the wall doesn't work and the molecules are also >>> out >>> > of the smaller box in several replica's simulations each with 100 ns. >>> > The only reason I can imagine is that the K=4184 KJ/(mol. nm^2 is >>> probably >>> > too low to keep the molecules inside the smaller box! I wonder if you >>> know >>> > any other potential reason? how can I find out the reason? >>> > >>> > Regards, >>> > Alex >>> > P.S. I am sure that I am using the flat-bottom restrain correctly as >>> the >>> > same approach worked for some other systems of mine previously. >>> > -- >>> > 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
Re: [gmx-users] Fat-bottom restrain
If the flat bottom restraint energy is zero, then that means that the restraints aren't being applied, or your predefined distance is not being exceeded. I doubt you would get binary zero values if it was the second option, so something is probably wrong with your syntax or your inclusion of the restraints Cheers, Billy On Wed., 11 Sep. 2019, 5:20 pm Billy Williams-Noonan, < billy.williams-noo...@monash.edu> wrote: > You may want to consider using smart-bottom restraints instead? > > Jokes aside, why does it matter if your molecules move into the next > periodic image? > > Cheers, > Billy > > On Wed., 11 Sep. 2019, 5:03 pm Alex, wrote: > >> Hi, >> >> Any comment, please? >> >> Thank you. >> Alex >> >> On Mon, Sep 9, 2019 at 10:22 PM Alex wrote: >> >> > Hi Mark, >> > >> > Thank you for your response. >> > Here are the part of options that gmx energy gives me out: >> > >> > 9 Coulomb-(SR)10 Coul.-recip. >> > 11 Flat-bottom-posres 12 Potential >> > 13 Kinetic-En. 14 Total-Energy15 Conserved-En >> > >> > >> > Energy Average Err.Est. RMSD Tot-Drift >> > >> > >> --- >> > Coulomb (SR) -8.4629e+061505041.75 -840.379 >> > (kJ/mol) >> > Coul. recip.12689.7 12109.811 -83.8453 >> > (kJ/mol) >> > Flat-bottom posres0 0 0 0 >> > (kJ/mol) >> > Potential-7.29781e+065403208.53 -3702.71 >> > (kJ/mol) >> > Kinetic En. 1.20527e+068.21912.61-12.144 >> > (kJ/mol) >> > Total Energy -6.09255e+06540 3942.5 -3714.84 >> > (kJ/mol) >> > Conserved En.-2.97263e+06 89 1.81911e+06 6.30101e+06 >> > (kJ/mol) >> > >> > As can be seen above the Flat-bottom posres energy is just zero during >> the >> > simulation; and even stiffening the force constant from 4184 KJ/(mol. >> nm^2) >> > to 4184000 KJ/(mol. nm^2) doesn't change anythings and the Flat-bottom >> > posres energy would remain absolutely zero! >> > >> > I rechecked everything and I don't see any problem with the way I have >> set >> > the flat-bottom restrain. >> > Any comment would be highly appreciated. >> > >> > Thank you, >> > Alex >> > >> > >> > >> > On Sat, Sep 7, 2019 at 10:47 AM Mark Abraham >> > wrote: >> > >> >> Hi, >> >> >> >> The total potential energy violating the restraints is reported, so you >> >> should see that there is an appropriate contribution there, and >> probably >> >> plan to stiffen the force constant. >> >> >> >> Mark >> >> >> >> On Fri., 6 Sep. 2019, 17:23 Alex, wrote: >> >> >> >> > Dear all, >> >> > Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to >> have a >> >> > smaller cubic box as semi-preamble walls inside a bigger cubic box so >> >> that >> >> > all molecules except water would stay inside the smaller box during >> the >> >> > simulation, however, the wall doesn't work and the molecules are also >> >> out >> >> > of the smaller box in several replica's simulations each with 100 ns. >> >> > The only reason I can imagine is that the K=4184 KJ/(mol. nm^2 is >> >> probably >> >> > too low to keep the molecules inside the smaller box! I wonder if you >> >> know >> >> > any other potential reason? how can I find out the reason? >> >> > >> >> > Regards, >> >> > Alex >> >> > P.S. I am sure that I am using the flat-bottom restrain correctly as >> the >> >> > same approach worked for some other systems of mine previously. >> >> > -- >> >> > 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. >> > -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] Fat-bottom restrain
You may want to consider using smart-bottom restraints instead? Jokes aside, why does it matter if your molecules move into the next periodic image? Cheers, Billy On Wed., 11 Sep. 2019, 5:03 pm Alex, wrote: > Hi, > > Any comment, please? > > Thank you. > Alex > > On Mon, Sep 9, 2019 at 10:22 PM Alex wrote: > > > Hi Mark, > > > > Thank you for your response. > > Here are the part of options that gmx energy gives me out: > > > > 9 Coulomb-(SR)10 Coul.-recip. > > 11 Flat-bottom-posres 12 Potential > > 13 Kinetic-En. 14 Total-Energy15 Conserved-En > > > > > > Energy Average Err.Est. RMSD Tot-Drift > > > > > --- > > Coulomb (SR) -8.4629e+061505041.75 -840.379 > > (kJ/mol) > > Coul. recip.12689.7 12109.811 -83.8453 > > (kJ/mol) > > Flat-bottom posres0 0 0 0 > > (kJ/mol) > > Potential-7.29781e+065403208.53 -3702.71 > > (kJ/mol) > > Kinetic En. 1.20527e+068.21912.61-12.144 > > (kJ/mol) > > Total Energy -6.09255e+06540 3942.5 -3714.84 > > (kJ/mol) > > Conserved En.-2.97263e+06 89 1.81911e+06 6.30101e+06 > > (kJ/mol) > > > > As can be seen above the Flat-bottom posres energy is just zero during > the > > simulation; and even stiffening the force constant from 4184 KJ/(mol. > nm^2) > > to 4184000 KJ/(mol. nm^2) doesn't change anythings and the Flat-bottom > > posres energy would remain absolutely zero! > > > > I rechecked everything and I don't see any problem with the way I have > set > > the flat-bottom restrain. > > Any comment would be highly appreciated. > > > > Thank you, > > Alex > > > > > > > > On Sat, Sep 7, 2019 at 10:47 AM Mark Abraham > > wrote: > > > >> Hi, > >> > >> The total potential energy violating the restraints is reported, so you > >> should see that there is an appropriate contribution there, and probably > >> plan to stiffen the force constant. > >> > >> Mark > >> > >> On Fri., 6 Sep. 2019, 17:23 Alex, wrote: > >> > >> > Dear all, > >> > Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to > have a > >> > smaller cubic box as semi-preamble walls inside a bigger cubic box so > >> that > >> > all molecules except water would stay inside the smaller box during > the > >> > simulation, however, the wall doesn't work and the molecules are also > >> out > >> > of the smaller box in several replica's simulations each with 100 ns. > >> > The only reason I can imagine is that the K=4184 KJ/(mol. nm^2 is > >> probably > >> > too low to keep the molecules inside the smaller box! I wonder if you > >> know > >> > any other potential reason? how can I find out the reason? > >> > > >> > Regards, > >> > Alex > >> > P.S. I am sure that I am using the flat-bottom restrain correctly as > the > >> > same approach worked for some other systems of mine previously. > >> > -- > >> > 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. > -- 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] Fat-bottom restrain
Hi, Any comment, please? Thank you. Alex On Mon, Sep 9, 2019 at 10:22 PM Alex wrote: > Hi Mark, > > Thank you for your response. > Here are the part of options that gmx energy gives me out: > > 9 Coulomb-(SR)10 Coul.-recip. > 11 Flat-bottom-posres 12 Potential > 13 Kinetic-En. 14 Total-Energy15 Conserved-En > > > Energy Average Err.Est. RMSD Tot-Drift > > --- > Coulomb (SR) -8.4629e+061505041.75 -840.379 > (kJ/mol) > Coul. recip.12689.7 12109.811 -83.8453 > (kJ/mol) > Flat-bottom posres0 0 0 0 > (kJ/mol) > Potential-7.29781e+065403208.53 -3702.71 > (kJ/mol) > Kinetic En. 1.20527e+068.21912.61-12.144 > (kJ/mol) > Total Energy -6.09255e+06540 3942.5 -3714.84 > (kJ/mol) > Conserved En.-2.97263e+06 89 1.81911e+06 6.30101e+06 > (kJ/mol) > > As can be seen above the Flat-bottom posres energy is just zero during the > simulation; and even stiffening the force constant from 4184 KJ/(mol. nm^2) > to 4184000 KJ/(mol. nm^2) doesn't change anythings and the Flat-bottom > posres energy would remain absolutely zero! > > I rechecked everything and I don't see any problem with the way I have set > the flat-bottom restrain. > Any comment would be highly appreciated. > > Thank you, > Alex > > > > On Sat, Sep 7, 2019 at 10:47 AM Mark Abraham > wrote: > >> Hi, >> >> The total potential energy violating the restraints is reported, so you >> should see that there is an appropriate contribution there, and probably >> plan to stiffen the force constant. >> >> Mark >> >> On Fri., 6 Sep. 2019, 17:23 Alex, wrote: >> >> > Dear all, >> > Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to have a >> > smaller cubic box as semi-preamble walls inside a bigger cubic box so >> that >> > all molecules except water would stay inside the smaller box during the >> > simulation, however, the wall doesn't work and the molecules are also >> out >> > of the smaller box in several replica's simulations each with 100 ns. >> > The only reason I can imagine is that the K=4184 KJ/(mol. nm^2 is >> probably >> > too low to keep the molecules inside the smaller box! I wonder if you >> know >> > any other potential reason? how can I find out the reason? >> > >> > Regards, >> > Alex >> > P.S. I am sure that I am using the flat-bottom restrain correctly as the >> > same approach worked for some other systems of mine previously. >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fat-bottom restrain
Hi Mark, Thank you for your response. Here are the part of options that gmx energy gives me out: 9 Coulomb-(SR)10 Coul.-recip. 11 Flat-bottom-posres 12 Potential 13 Kinetic-En. 14 Total-Energy15 Conserved-En Energy Average Err.Est. RMSD Tot-Drift --- Coulomb (SR) -8.4629e+061505041.75 -840.379 (kJ/mol) Coul. recip.12689.7 12109.811 -83.8453 (kJ/mol) Flat-bottom posres0 0 0 0 (kJ/mol) Potential-7.29781e+065403208.53 -3702.71 (kJ/mol) Kinetic En. 1.20527e+068.21912.61-12.144 (kJ/mol) Total Energy -6.09255e+06540 3942.5 -3714.84 (kJ/mol) Conserved En.-2.97263e+06 89 1.81911e+06 6.30101e+06 (kJ/mol) As can be seen above the Flat-bottom posres energy is just zero during the simulation; and even stiffening the force constant from 4184 KJ/(mol. nm^2) to 4184000 KJ/(mol. nm^2) doesn't change anythings and the Flat-bottom posres energy would remain absolutely zero! I rechecked everything and I don't see any problem with the way I have set the flat-bottom restrain. Any comment would be highly appreciated. Thank you, Alex On Sat, Sep 7, 2019 at 10:47 AM Mark Abraham wrote: > Hi, > > The total potential energy violating the restraints is reported, so you > should see that there is an appropriate contribution there, and probably > plan to stiffen the force constant. > > Mark > > On Fri., 6 Sep. 2019, 17:23 Alex, wrote: > > > Dear all, > > Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to have a > > smaller cubic box as semi-preamble walls inside a bigger cubic box so > that > > all molecules except water would stay inside the smaller box during the > > simulation, however, the wall doesn't work and the molecules are also out > > of the smaller box in several replica's simulations each with 100 ns. > > The only reason I can imagine is that the K=4184 KJ/(mol. nm^2 is > probably > > too low to keep the molecules inside the smaller box! I wonder if you > know > > any other potential reason? how can I find out the reason? > > > > Regards, > > Alex > > P.S. I am sure that I am using the flat-bottom restrain correctly as the > > same approach worked for some other systems of mine previously. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fat-bottom restrain
Hi, The total potential energy violating the restraints is reported, so you should see that there is an appropriate contribution there, and probably plan to stiffen the force constant. Mark On Fri., 6 Sep. 2019, 17:23 Alex, wrote: > Dear all, > Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to have a > smaller cubic box as semi-preamble walls inside a bigger cubic box so that > all molecules except water would stay inside the smaller box during the > simulation, however, the wall doesn't work and the molecules are also out > of the smaller box in several replica's simulations each with 100 ns. > The only reason I can imagine is that the K=4184 KJ/(mol. nm^2 is probably > too low to keep the molecules inside the smaller box! I wonder if you know > any other potential reason? how can I find out the reason? > > Regards, > Alex > P.S. I am sure that I am using the flat-bottom restrain correctly as the > same approach worked for some other systems of mine previously. > -- > 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.
