[gmx-users] implicit solvent error

[Alex]

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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