[gmx-users] Correct .mdp file for Amber99SB-ILDN ff implementation in Gromacs

[João Henriques]

> I was wondering if I should modify any terms because of using Gromacs
package?

It's good practice to set your key parameters as close as possible to
theirs. I am not familiar with Desmond, but I assume many of its parameters
have similar counterparts in Gromacs. If you plan on (significantly)
modifying any parameters, you necessarily need to perform a sanity check
and validate your results.

To me, and this is my personal opinion, there are some parameters in your
email that seem a bit strange. Why 1 femtosecond integration time for the
equilibration? 2 fs with LINCS should work fine. Why do you set two
different Fourier spacings? Plus, why set the last one (the one that is
effectively used) to zero? Where did you get that 1.05 for the rlist? Is
that 0.05 going to make any difference? Also, double check the pressure and
temperature coupling constants. Finally, why are you generating an initial
temperature of 50K and then have it coupled to 310 K?

These are just a few issues that come to mind after a quick read of your
email. There may be others, and I may also be wrong in my assessment... I
personally believe that there is no single recipe to performing
simulations, and I find that it is always better to modify only what you
need and understand, instead of following someone's work blindly. After
all, you need you understand what and why you do it and, unless you're
trying to replicate their work, no single set of parameters should be
absolutely "right". You need, of course, to be sensible when changing them
and check/validate your results afterwards.

Hope it helps,
Best regards,
João

On Wed, Jul 13, 2016 at 11:34 PM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> Dear Gromacs-users,
>
> I am interested in simulation of protein-ligand system.
>
> To do so, I have chosen the amber99sb-ildn force field.
>
> Reading through the original paper on this force filed by D.E.Shaw group
> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/) I have made the
> following equilibriu,.mdp and production-run.mdp files. I am not sure of
> it, though. Please correct me if I am wrong.
>
> The authors have used Desmond package not Gromacs for their simulations.
> I was wondering if I should modify any terms because of using Gromacs
> package?
> (This is the case for using charmm force field in Gromacs).
>
> I read other posts in gromacs list but I could not get any clear answer for
> this.
>
> Thanks in advance for your comments
> Cheers
> Mohsen
>
>
> for Equilibrium.mdp, I made:
>
> define                   =
>
> ; RUN CONTROL PARAMETERS
> integrator               = md         ;
> tinit                       = 0            ;
> dt                          = 0.001     ; 1 femtosecond time step for
> integration
> nsteps                   = 500000   ; 1 ns
>
> ; OUTPUT CONTROL OPTIONS
> nstxout                  = 0          ; Writing full precision coordinates
> nstvout                  = 0          ; Writing velocities
> nstfout                   = 0          ; writing forces
> nstlog                    = 2500     ; Writing to the log file
> nstenergy               = 2500    ; Writing out energy information
> nstxtcout                = 2500    ; Writing coordinates every 5 ps
> energygrps             = Protein   ligand  Water_and_ions
> xtc_precision          = 1000
> xtc-grps                 = System
>
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist                  = 10
> ns-type                = Grid
> pbc                      = xyz
> rlist                      = 1.05
> cutoff-scheme       = Verlet
> nstcalclr                = 1
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype          = PME
> rcoulomb               = 1.0
> fourierspacing        = 0.1
> vdw-type               = cut-off
> rvdw                     = 1.0
> optimize_fft           = yes
> fourierspacing           = 0
> fourier-nx               = 32
> fourier-ny               = 32
> fourier-nz               = 32
> pme-order                = 4
>
> ; Temperature coupling
> Tcoupl                   = v-rescale            ; in the original paper it
> is Nose-Hoover thermostat
> tc-grps                   = Protein_ligand  Water_and_ions
> tau_t                      = 1.0      1.0
> ref_t                       = 310      310
>
> ; Pressure coupling
> Pcoupl                   = nose-hoover
> Pcoupltype             = isotropic
> tau_p                     = 5.5
> compressibility       = 4.5e-5
> ref_p                     = 1.00
> refcoord_scaling      = com
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel                    = yes    ; Assign velocities to particles by
> taking them randomly from a Maxwell distribution
> gen_temp                 = 50.0  ; Temperature to generate corresponding
> Maxwell distribution
> gen_seed                 = 1235   ; Seed for (semi) random number
> generation.
>
> ; OPTIONS FOR BONDS
> constraint-algorithm     = SHAKE
> constraints                  = h-bonds
>
>
> and for production-run.mdp, I just change the
>
> dt                               = 0.002     ; 1 femtosecond time step for
> integration
> constraint-algorithm     = LINCS
> constraints                  = all-bonds
> gen_vel                       = no
>
>
>
>
>
> --
> *Rewards work better than punishment ...*
> --
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