[gmx-users] ff99SB-ILDN and .mdp parameters

[Timofey Tyugashev]

Also I have some doubts about proper mdp parameters to use for AMBER 
ff99SB-ILDN. GROMACS site recently updated ones for CHARMM 
(http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM), 
but not for AMBER.
Currently I use the following options for MD run:
> continuation    = yes           ; first dynamics run
> constraint_algorithm = lincs
> constraints     = all-bonds
> lincs_iter      = 1             ; default
> lincs_order     = 4             ; default
> ; Neighborsearching
> cutoff-scheme   = Verlet
> ns_type         = grid
> nstlist         = 40
> rcoulomb	    = 1.0		; Short-range electrostatic cut-off
> rvdw		    = 1.0		; Short-range Van der Waals cut-off
> rlist			= 1.0		; Short-range neighbor list
> rlistlong		= 1.05		; Long-range neighbor list
> ; Electrostatics
> coulombtype     = PME       ; Particle Mesh Ewald for long-range electrostatics
> pme_order       = 4         ; cubic interpolation
> fourierspacing  = 0.16      ; grid spacing for FFT
> ; Temperature coupling
> tcoupl      = V-rescale                     ; Berendsen-modified
> tc-grps     = Protein_DNA Water_and_ions    ; two groups
> tau_t       = 0.1   0.1                     ; time constant, in ps
> ref_t       = 300   300                     ; reference temperature, one for each group, in K
> ; Pressure coupling
> pcoupl      = Parrinello-Rahman             ; pressure coupling is on for NPT
> pcoupltype  = isotropic                     ; uniform scaling of box vectors
> tau_p       = 2.0                           ; time constant, in ps
> ref_p       = 1.0                           ; reference pressure, in bar
> compressibility = 4.5e-5                    ; isothermal compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc         = xyz       ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel     = no        ; assign velocities from Maxwell distribution
>


Paper for this FF provides the following parameters for computation 
set-up and I tried to implement them in .mdp, but I'm not sure how 
correct my interpretation is.

    Each system was equilibrated at 300 K and 1 atm with 2.4 ns of MD
    simulation in the NPT ensemble. Then, MD simulations were carried
    out in the NVT ensemble for 720 ns using the Nosé-Hoover thermostat
    with a relaxation time of 1 ps. All simulations were performed using
    the Desmond MD program^16
    <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b16> version
    2.1.1.0 and either the Amber ff99SB^7
    <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b7> or the
    modified Amber ff99SB force field described herein, which we have
    termed ff99SB-ILDN. All bonds involving hydrogen atoms were
    constrained with the SHAKE algorithm.^17
    <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b17> A cutoff
    of 10 Å was used for the Lennard-Jones interaction and the
    short-range electrostatic interactions. The smooth particle mesh
    Ewald method^18
    <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b18> with a
    32 × 32 × 32 grid and a fourth-order interpolation scheme was used
    to compute the long-range electrostatic interactions. The pairlists
    were updated every 10 fs with a cutoff of 10.5 Å. We used a
    multistep RESPA scheme^19
    <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b19> for the
    integration of the equations of motion with timesteps of 2.0, 2.0,
    and 6.0 fs for the bonded, short-range nonbonded, and long-range
    nonbonded interactions, respectively. To check for potential biases
    introduced by long-range interactions between peptides in periodic
    images, we repeated these simulations for four of the amino acids
    (Xaa: Ile, Leu, Asp, and Asn) using a larger box with side length 37
    Å. We found that the results of these control simulations were
    within error of those using the smaller box sizes.


If understand the manual correctly, the Verlet option for cut-off scheme 
overrides rlist settings anyway and autotunes it.