[gmx-users] Using custom potential for electrostatics between protein and water
Aram Davtyan
davtyan.aram at gmail.com
Wed Dec 6 14:57:40 CET 2017
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
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