[gmx-users] Fwd: Implicit solvent simulations using GROMACS-2016

[Mark Abraham]

Hi,

Implicit solvation has been untested since 4.5.7, unfortunately, and has
been removed after we release GROMACS 2018. As the comment suggests,
nothing is particularly trustworthy since 4.5.7, but anecdotally,
simulations running on a single rank have been working fine (so for a
multi-sim of N simulations, use N ranks).

Mark

On Wed, Apr 4, 2018 at 11:27 PM Sai Pooja <saipooja at gmail.com> wrote:

> Hi,
>
> I am trying to run an implicit solvent (water) simulation for a protein. I
> am able to successfully run one with gromacs 4.5 with charmm forcefield and
> infinite cutoffs with the sd integrator. When I follow the same steps and
> try to do the same with the newer version i.e. gromacs-2016.1 (same setup
> except cutoff-scheme = group), I am unable to equilibrate the system at
> constant temperature. I have tried timesteps from 0.002 to 0.0005.
> Temperature explodes within the first 100 steps. I am at a loss for
> reasons. Is it still possible to simulate implicit solvent systems with
> gromacs?
>
> Forcefield: CHARMM (with cmap)
> Here are the mdp file parameters:
> define                  = -DPOSRES
>
> integrator               = sd
> dt                       = 0.001
> nsteps                   = 1000
>
> cutoff_scheme = group
> vdwtype            = cutoff
> ns_type              =  simple
> nstlist                 = 0
> rlist                     = 0
> rgbradii                  = 0
> rcoulomb          = 0
> rvdw                  = 0
> coulombtype    = cutoff
> pbc                      = no
> comm-mode      = angular
> comm-grps        = Protein
> implicit_solvent = GBSA
> gb_algorithm      = OBC
> sa_algorithm = ace_approximation
> sa_surface_tension      = 2.25936
>
> ; OUTPUT CONTROL OPTIONS
> nstxout                  = 1 ; ast frame (coordinates)
> nstvout                  = 500   ;  (velocities)
> nstfout                  = 500   ; No output, except for last frame
> (forces)
> nstlog                   = 1  ; Write every step to the log
> nstenergy                = 500  ; Write energies at every step
> xtc_grps                 = Protein
> nstxtcout                = 1   ; Do not write a compressed trajectory
> energygrps               = Protein  ; Write energy information separately
> for these groups
> ; Temperature coupling
> tcoupl                   = no
> tc-grps                  = Protein
> tau_t                    = 2         ; 1/91 2010 gromacs charm paper?does
> not work
> ref_t                    = 300
> gen_vel                  = yes
> gen_temp                 = 300
>
> ; Pressure coupling
> pcoupl                   = no
> tau_p                    = 1
> ref_p                    = 1
> compressibility          = 4.5e-5
> refcoord_scaling         = com
>
> ; OPTIONS FOR BONDS
> constraints              = all-bonds
>
> gmx_mpi mdrun -deffnm proteinsim_ -multi 24
>
> The simulations start but the temperature rises very quickly and then the
> simulation explodes. I have explored various options like trying different
> temperatures, changing tau_t to slow down and/or speed up temperature
> equilibration and tried different timesteps but without much success.
>
> If anyone has a benchmark for running implicit solvent simulations with the
> new gromacs (post 4.5), I would be very grateful.
>
> I also see these comments in the logfile:
> >>>
> Using SIMD all-vs-all kernels.
>
> This is simulation 0 out of 24 running as a composite GROMACS
> multi-simulation job. Setup for this simulation:
>
> Using 1 MPI process
>
>
> Your simulation settings would have triggered the efficient all-vs-all
> kernels in GROMACS 4.5, but these have not been implemented in GROMACS
> 4.6 and 5.x. If performance is important, please use GROMACS 4.5.7
> or try cutoff-scheme = Verlet.
> <<<
> Does this mean that the older version is recommended for implicit solvent
> simulations?
>
>
> Thanks,
> P
> --
> "Tiger got to hunt, bird got to fly; Man got to sit and wonder, 'Why, why,
> why?' Tiger got to sleep, bird got to land; Man got to tell himself he
> understand." --KV
>
>
>
> --
> "Tiger got to hunt, bird got to fly; Man got to sit and wonder, 'Why, why,
> why?' Tiger got to sleep, bird got to land; Man got to tell himself he
> understand." --KV
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