[gmx-users] implicit solvent error
Chhaya Singh
chhayasingh014 at gmail.com
Sun Jun 24 10:06:26 CEST 2018
sorry i attached a wrong file.
this is my inputs about the implcit solvent
integrator = md
dt = 0.005 ; ps !
nsteps = 20000000 ; total 10 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 = simple
constraints = all-bonds
lincs_order = 4
lincs_iter = 1
lincs-warnangle = 30
Tcoupl = v-rescale
tau_t = 1.0
tc-grps = Protein
ref_t = 300
Pcoupl = no
gen_vel = yes
gen_temp = 300
gen_seed = 173529
;http://www.mail-archive.com/gmx-users@gromacs.org/msg20866.html
;mine addition
comm_mode = angular
nstcomm = 10
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = gbsa
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = OBC ;Still
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 5
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension = -1
1,1 Top
On 24 June 2018 at 13:17, Alex <nedomacho at gmail.com> wrote:
> Your EM is unrelated to dynamics. I mean, it could, but we don't know
> anything about your simulated system. I am of course assuming that your MPI
> setup is optimal for gmx and you actually get to use those 16 threads,
> assuming those aren't an emulation of some sort.
>
>
>
> On 6/24/2018 1:33 AM, Chhaya Singh wrote:
>
>> 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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