[gmx-users] implicit solvent error
nedomacho at gmail.com
Sun Jun 24 09:30:07 CEST 2018
This input has no information about implicit solvent and a simple google
search immediately yields mdp examples using gbsa. As far as performance
is concerned, we don't know the specs of your machine or the size of
your system. With cutoff electrostatics and a cutoff of 5 nm, one can
expect quite a bit of scaling with system size beyond linear.
On 6/24/2018 1:04 AM, Chhaya Singh wrote:
> I am trying to simulate a protein in an implicit solvent in groamcs using
> amber ff99sb ildn .
> the mdpfile that I am using is I have shown below:
> integrator = md
> dt = 0.001 ;0.005 ; ps !
> nsteps = 5000000 ; total 5 ns.
> nstlog = 5000
> nstxout = 0 ;1000
> nstvout = 0 ;1000
> nstfout = 0 ;1000
> nstxtcout = 5000
> nstenergy = 5000
> nstlist = 10
> cutoff-scheme = group
> rlist = 5
> rvdw = 5
> rcoulomb = 5
> coulombtype = cut-off
> vdwtype = cut-off
> bd_fric = 0
> ;ld_seed = -1
> pbc = no
> ns_type = grid ;simple => gives domain decomposition error
> constraints = all-bonds
> lincs_order = 4
> lincs_iter = 1
> lincs-warnangle = 30
> Tcoupl = v-rescale
> tau_t = 1.0
> tc-grps = Protein
> ref_t = 310
> This is the mdp file that I am using for equilibration and production run,
> if there is anything that I can fix in mdp file please let me know.
> I am getting very less speed using an implicit solvent in gromacs.
> is there any way to increase the speed.
> the speed right now I am getting is 0.47- 0.74 ns /day using one node.
> please help.
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