[gmx-users] Using custom potential for electrostatics between protein and water

Aram Davtyan davtyan.aram at gmail.com
Wed Dec 6 15:39:09 CET 2017


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-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Aram
> Davtyan <davtyan.aram at gmail.com>
> Sent: 06 December 2017 13:57:17
> To: gromacs.org_gmx-users at 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.aram at 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-request at gromacs.org.
> > >
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Wed, 06 Dec 2017 00:46:51 +0000
> > From: Mark Abraham <mark.j.abraham at gmail.com>
> > To: gmx-users at gromacs.org
> > Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: Re: [gmx-users] Using custom potential for electrostatics
> >         between protein and water
> > Message-ID:
> >         <CAMNuMAR4K=RxxJuo8X0qHPt3c6Jpnm2PSVXy3RP8_Vg4ipgH+w at 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.aram at 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-request at 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-request at 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: adavtyan at rice.edu <adavtyan at 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-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 6 Dec 2017 14:02:37 +0000
> From: Srinivasa Ramisetti <S.B.Ramisetti at leeds.ac.uk>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>, "
> gmx-users at gromacs.org"
>         <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Using custom potential for electrostatics
>         between protein and water
> Message-ID:
>         <DB5PR03MB151234574BCD33FCF839C47EE4320 at 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-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Aram
> Davtyan <davtyan.aram at gmail.com>
> Sent: 06 December 2017 13:57:17
> To: gromacs.org_gmx-users at 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.aram at 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-request at gromacs.org.
> > >
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Wed, 06 Dec 2017 00:46:51 +0000
> > From: Mark Abraham <mark.j.abraham at gmail.com>
> > To: gmx-users at gromacs.org
> > Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: Re: [gmx-users] Using custom potential for electrostatics
> >         between protein and water
> > Message-ID:
> >         <CAMNuMAR4K=RxxJuo8X0qHPt3c6Jpnm2PSVXy3RP8_Vg4ipgH+w at 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.aram at 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
> > > --
>


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