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

[Mark Abraham]

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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