Ok, so I tried the following. I have changed cutoff-scheme=verlet" to "cutoff-scheme=group" and "rlist = 1.2" to "rlist = 1.4".
Now I get the following working when trying to generate the TPR: WARNING 1 [file md_energygrp-table_group.mdp]: The sum of the two largest charge group radii (32.555389) is larger than rlist (1.400000) Thanks, Aram Hi Arm, > > > As mark suggested you have to replace "cutoff-scheme=verlet" to > "cutoff-scheme=group". > > > Srinivasa > > ________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Aram > Davtyan <davtyan.a...@gmail.com> > Sent: 06 December 2017 13:57:17 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Using custom potential for electrostatics between > protein and water > > Hi, > > Yeah, but first of all it doesn't give me an error and, second, how do I > transition from verlet to group cutoff scheme in order for the custom > tables to work? > > In other words, what specific changes should I make for GROMACS to use the > modified tables, and, at the same time, when the > `table6-12_Protein_Water.xvg` is the same as `table6-12.xvg` I get the same > answer as before? > > Thanks, > > Aram > > > > > Hi, > > > > User tables for nonbonded interactions, including pme-user are only > > supported with the group cutoff scheme, not verlet. grompp should give a > > fatal error to tell you that, sorry. > > > > Mark > > > > On Wed, Dec 6, 2017 at 10:50 AM Aram Davtyan <davtyan.a...@gmail.com> > > wrote: > > > > > Hello, > > > > > > I am trying to use a custom electrostatic potential between protein and > > > water, with protein-protein and water-water potentials remaining the > > same. > > > > > > I tried running the simulation with the following input script: > > > > > > define = -DPOSRES ; position restrain for protein > > > integrator = md > > > dt = 0.002 > > > nsteps = 10000 ; 2ns > > > nstlog = 1000 > > > nstxout = 5000 > > > nstvout = 5000 > > > nstfout = 5000 > > > nstcalcenergy = 100 > > > nstenergy = 1000 > > > ; > > > cutoff-scheme = Verlet > > > nstlist = 20 > > > rlist = 1.2 > > > coulombtype = pme-user > > > rcoulomb = 1.2 > > > vdwtype = Cut-off > > > vdw-modifier = Force-switch > > > rvdw_switch = 1.0 > > > rvdw = 1.2 > > > ; > > > energygrps = Protein Water Ion > > > energygrp-table = Protein Water > > > ; > > > tcoupl = Nose-Hoover > > > tc_grps = Protein Non-Protein > > > tau_t = 1.0 1.0 > > > ref_t = 300.0 300.0 > > > ; > > > pcoupl = Parrinello-Rahman > > > pcoupltype = isotropic > > > tau_p = 5.0 > > > compressibility = 4.5e-5 > > > ref_p = 1.0 > > > ; > > > ld_seed = 0 > > > ; > > > constraints = h-bonds > > > constraint_algorithm = LINCS > > > continuation = yes > > > ; > > > nstcomm = 100 > > > comm_mode = linear > > > comm_grps = Protein Non-Protein > > > ; > > > refcoord_scaling = com > > > > > > I have the following tables: `table6-12.xvg` and > > > `table6-12_Protein_Water.xvg` in the directory and run the simulation > > with > > > the following command lines > > > > > > gmx grompp -f md_energygrp-table.mdp -c npt.gro -t npt.cpt -p topol.top > > -o > > > md_0_5.tpr > > > gmx mdrun -deffnm md_0_5 -reprod -table table6-12.xvg -tablep > > table6-12.xvg > > > > > > To test I set the electrostatic potential (f(r) and f'(r)) to zero in > > > `table6-12_Protein_Water.xvg` file. However, I find that the energies > > > calculated at the first step are identical to the case when custom > > > potentials are not used. What am I doing wrong? > > > > > > Thank you in advance, > > > > > > Aram > > > -- > > > 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. > > > > > > > > > ------------------------------ > > > > Message: 5 > > Date: Wed, 06 Dec 2017 00:46:51 +0000 > > From: Mark Abraham <mark.j.abra...@gmail.com> > > To: gmx-us...@gromacs.org > > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: Re: [gmx-users] Using custom potential for electrostatics > > between protein and water > > Message-ID: > > <CAMNuMAR4K=RxxJuo8X0qHPt3c6Jpnm2PSVXy3RP8_Vg4ipgH+w@mail. > > gmail.com> > > Content-Type: text/plain; charset="UTF-8" > > > > Hi, > > > > User tables for nonbonded interactions, including pme-user are only > > supported with the group cutoff scheme, not verlet. grompp should give a > > fatal error to tell you that, sorry. > > > > Mark > > > > On Wed, Dec 6, 2017 at 10:50 AM Aram Davtyan <davtyan.a...@gmail.com> > > wrote: > > > > > Hello, > > > > > > I am trying to use a custom electrostatic potential between protein and > > > water, with protein-protein and water-water potentials remaining the > > same. > > > > > > I tried running the simulation with the following input script: > > > > > > define = -DPOSRES ; position restrain for protein > > > integrator = md > > > dt = 0.002 > > > nsteps = 10000 ; 2ns > > > nstlog = 1000 > > > nstxout = 5000 > > > nstvout = 5000 > > > nstfout = 5000 > > > nstcalcenergy = 100 > > > nstenergy = 1000 > > > ; > > > cutoff-scheme = Verlet > > > nstlist = 20 > > > rlist = 1.2 > > > coulombtype = pme-user > > > rcoulomb = 1.2 > > > vdwtype = Cut-off > > > vdw-modifier = Force-switch > > > rvdw_switch = 1.0 > > > rvdw = 1.2 > > > ; > > > energygrps = Protein Water Ion > > > energygrp-table = Protein Water > > > ; > > > tcoupl = Nose-Hoover > > > tc_grps = Protein Non-Protein > > > tau_t = 1.0 1.0 > > > ref_t = 300.0 300.0 > > > ; > > > pcoupl = Parrinello-Rahman > > > pcoupltype = isotropic > > > tau_p = 5.0 > > > compressibility = 4.5e-5 > > > ref_p = 1.0 > > > ; > > > ld_seed = 0 > > > ; > > > constraints = h-bonds > > > constraint_algorithm = LINCS > > > continuation = yes > > > ; > > > nstcomm = 100 > > > comm_mode = linear > > > comm_grps = Protein Non-Protein > > > ; > > > refcoord_scaling = com > > > > > > I have the following tables: `table6-12.xvg` and > > > `table6-12_Protein_Water.xvg` in the directory and run the simulation > > with > > > the following command lines > > > > > > gmx grompp -f md_energygrp-table.mdp -c npt.gro -t npt.cpt -p topol.top > > -o > > > md_0_5.tpr > > > gmx mdrun -deffnm md_0_5 -reprod -table table6-12.xvg -tablep > > table6-12.xvg > > > > > > To test I set the electrostatic potential (f(r) and f'(r)) to zero in > > > `table6-12_Protein_Water.xvg` file. However, I find that the energies > > > calculated at the first step are identical to the case when custom > > > potentials are not used. What am I doing wrong? > > > > > > Thank you in advance, > > > > > > Aram > > > -- > > > 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. > > > > End of gromacs.org_gmx-users Digest, Vol 164, Issue 19 > > ****************************************************** > > > > > > -- > Aram Davtyan, Ph.D. > Center for Theoretical Biological Physics > Rice University > E-mail: adavt...@rice.edu <adavt...@uchicago.edu> > Phone: (919)265-8369 > -- > 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. > > > ------------------------------ > > Message: 3 > Date: Wed, 6 Dec 2017 14:02:37 +0000 > From: Srinivasa Ramisetti <s.b.ramise...@leeds.ac.uk> > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se>, " > gmx-us...@gromacs.org" > <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] Using custom potential for electrostatics > between protein and water > Message-ID: > <DB5PR03MB151234574BCD33FCF839C47EE4320@DB5PR03MB1512. > eurprd03.prod.outlook.com> > > Content-Type: text/plain; charset="us-ascii" > > Hi Arm, > > > As mark suggested you have to replace "cutoff-scheme=verlet" to > "cutoff-scheme=group". > > > Srinivasa > > ________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Aram > Davtyan <davtyan.a...@gmail.com> > Sent: 06 December 2017 13:57:17 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Using custom potential for electrostatics between > protein and water > > Hi, > > Yeah, but first of all it doesn't give me an error and, second, how do I > transition from verlet to group cutoff scheme in order for the custom > tables to work? > > In other words, what specific changes should I make for GROMACS to use the > modified tables, and, at the same time, when the > `table6-12_Protein_Water.xvg` is the same as `table6-12.xvg` I get the same > answer as before? > > Thanks, > > Aram > > > > > Hi, > > > > User tables for nonbonded interactions, including pme-user are only > > supported with the group cutoff scheme, not verlet. grompp should give a > > fatal error to tell you that, sorry. > > > > Mark > > > > On Wed, Dec 6, 2017 at 10:50 AM Aram Davtyan <davtyan.a...@gmail.com> > > wrote: > > > > > Hello, > > > > > > I am trying to use a custom electrostatic potential between protein and > > > water, with protein-protein and water-water potentials remaining the > > same. > > > > > > I tried running the simulation with the following input script: > > > > > > define = -DPOSRES ; position restrain for protein > > > integrator = md > > > dt = 0.002 > > > nsteps = 10000 ; 2ns > > > nstlog = 1000 > > > nstxout = 5000 > > > nstvout = 5000 > > > nstfout = 5000 > > > nstcalcenergy = 100 > > > nstenergy = 1000 > > > ; > > > cutoff-scheme = Verlet > > > nstlist = 20 > > > rlist = 1.2 > > > coulombtype = pme-user > > > rcoulomb = 1.2 > > > vdwtype = Cut-off > > > vdw-modifier = Force-switch > > > rvdw_switch = 1.0 > > > rvdw = 1.2 > > > ; > > > energygrps = Protein Water Ion > > > energygrp-table = Protein Water > > > ; > > > tcoupl = Nose-Hoover > > > tc_grps = Protein Non-Protein > > > tau_t = 1.0 1.0 > > > ref_t = 300.0 300.0 > > > ; > > > pcoupl = Parrinello-Rahman > > > pcoupltype = isotropic > > > tau_p = 5.0 > > > compressibility = 4.5e-5 > > > ref_p = 1.0 > > > ; > > > ld_seed = 0 > > > ; > > > constraints = h-bonds > > > constraint_algorithm = LINCS > > > continuation = yes > > > ; > > > nstcomm = 100 > > > comm_mode = linear > > > comm_grps = Protein Non-Protein > > > ; > > > refcoord_scaling = com > > > > > > I have the following tables: `table6-12.xvg` and > > > `table6-12_Protein_Water.xvg` in the directory and run the simulation > > with > > > the following command lines > > > > > > gmx grompp -f md_energygrp-table.mdp -c npt.gro -t npt.cpt -p topol.top > > -o > > > md_0_5.tpr > > > gmx mdrun -deffnm md_0_5 -reprod -table table6-12.xvg -tablep > > table6-12.xvg > > > > > > To test I set the electrostatic potential (f(r) and f'(r)) to zero in > > > `table6-12_Protein_Water.xvg` file. However, I find that the energies > > > calculated at the first step are identical to the case when custom > > > potentials are not used. What am I doing wrong? > > > > > > Thank you in advance, > > > > > > Aram > > > -- > > > 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. > > > > > > > > > ------------------------------ > > > > Message: 5 > > Date: Wed, 06 Dec 2017 00:46:51 +0000 > > From: Mark Abraham <mark.j.abra...@gmail.com> > > To: gmx-us...@gromacs.org > > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: Re: [gmx-users] Using custom potential for electrostatics > > between protein and water > > Message-ID: > > <CAMNuMAR4K=RxxJuo8X0qHPt3c6Jpnm2PSVXy3RP8_Vg4ipgH+w@mail. > > gmail.com> > > Content-Type: text/plain; charset="UTF-8" > > > > Hi, > > > > User tables for nonbonded interactions, including pme-user are only > > supported with the group cutoff scheme, not verlet. grompp should give a > > fatal error to tell you that, sorry. > > > > Mark > > > > On Wed, Dec 6, 2017 at 10:50 AM Aram Davtyan <davtyan.a...@gmail.com> > > wrote: > > > > > Hello, > > > > > > I am trying to use a custom electrostatic potential between protein and > > > water, with protein-protein and water-water potentials remaining the > > same. > > > > > > I tried running the simulation with the following input script: > > > > > > define = -DPOSRES ; position restrain for protein > > > integrator = md > > > dt = 0.002 > > > nsteps = 10000 ; 2ns > > > nstlog = 1000 > > > nstxout = 5000 > > > nstvout = 5000 > > > nstfout = 5000 > > > nstcalcenergy = 100 > > > nstenergy = 1000 > > > ; > > > cutoff-scheme = Verlet > > > nstlist = 20 > > > rlist = 1.2 > > > coulombtype = pme-user > > > rcoulomb = 1.2 > > > vdwtype = Cut-off > > > vdw-modifier = Force-switch > > > rvdw_switch = 1.0 > > > rvdw = 1.2 > > > ; > > > energygrps = Protein Water Ion > > > energygrp-table = Protein Water > > > ; > > > tcoupl = Nose-Hoover > > > tc_grps = Protein Non-Protein > > > tau_t = 1.0 1.0 > > > ref_t = 300.0 300.0 > > > ; > > > pcoupl = Parrinello-Rahman > > > pcoupltype = isotropic > > > tau_p = 5.0 > > > compressibility = 4.5e-5 > > > ref_p = 1.0 > > > ; > > > ld_seed = 0 > > > ; > > > constraints = h-bonds > > > constraint_algorithm = LINCS > > > continuation = yes > > > ; > > > nstcomm = 100 > > > comm_mode = linear > > > comm_grps = Protein Non-Protein > > > ; > > > refcoord_scaling = com > > > > > > I have the following tables: `table6-12.xvg` and > > > `table6-12_Protein_Water.xvg` in the directory and run the simulation > > with > > > the following command lines > > > > > > gmx grompp -f md_energygrp-table.mdp -c npt.gro -t npt.cpt -p topol.top > > -o > > > md_0_5.tpr > > > gmx mdrun -deffnm md_0_5 -reprod -table table6-12.xvg -tablep > > table6-12.xvg > > > > > > To test I set the electrostatic potential (f(r) and f'(r)) to zero in > > > `table6-12_Protein_Water.xvg` file. However, I find that the energies > > > calculated at the first step are identical to the case when custom > > > potentials are not used. What am I doing wrong? > > > > > > Thank you in advance, > > > > > > Aram > > > -- > -- 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.