[gmx-users] implicit solvent error

[Chhaya Singh]

Hi,
I have attached the energy minimization mdp file.
please look through it .



cpp                 =
/lib/cpp                                                 ; prepocessor of
the current machine
define              =
-DFLEXIBLE                                               ; -DPOSRES,
-DPOSRES_IONS ;DFLEX_SPC; FLEXible SPC and POSition REStraints

integrator          =
steep                                                    ; steepest descent
algorithm
dt                  =
0.005                                                    ; time step in ps
nsteps              =
5000                                                     ; number of steps

emtol               =
100                                                      ; convergence
criterion
emstep              =
0.05                                                     ; intial step size
constraints           = none
constraint-algorithm  = lincs
unconstrained-start   =
no                                                      ; Do not constrain
the start configuration
;shake_tol           = 0.0001
nstlist             =
0                                                        ; step frequency
for updating neighbour list
ns_type             =
simple                                                   ; grid ; method
for nighbour searching (?)
nstxout             =
100                                                      ; frequency for
writing coords to output
nstvout             =
100                                                      ; frequency for
writing velocities to output
nstfout             =  0    ; frequency for writing forces to output
nstlog              =  100    ; frequency for writing energies to log file
nstenergy           =  100  ; frequency for writing energies to energy file
nstxtcout           =  0    ; frequency for writing coords to xtc traj
xtc_grps            =  system ; group(s) whose coords are to be written in
xtc traj
energygrps          =  system ; group(s) whose energy is to be written in
energy file
pbc                 =  no    ; use pbc
rlist               =  1.4    ; cutoff (nm)
coulombtype         =  cutoff ; truncation for minimisation, with large
cutoff
rcoulomb            =  1.4
vdwtype             =  cut-off  ; truncation for minimisation, with large
cutoff
rvdw                =  1.4
nstcomm             =  0  ; number of steps for centre of mass motion
removal (in vacuo only!)
Tcoupl              =  no
Pcoupl              =  no
"min-implicit.mdp" 40L,
2616C
1,1           Top



the system I am using has the following information:
PBS -l select=1:ncpus=16:mpiprocs=16
#PBS -l walltime=24:00:00



On 24 June 2018 at 13:00, Alex <nedomacho at gmail.com> wrote:

> 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.
>
> Alex
>
>
>
> On 6/24/2018 1:04 AM, Chhaya Singh wrote:
>
>> Hi,
>>
>> 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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