[gmx-users] Re: single point calculation with gromacs

[fantasticqhl]

Dear Justin,

*Thanks very much for your reply! Here is my minim.mdp I used:*


/; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator      = steep         ; Algorithm (steep = steepest descent
minimization)
emtol           = 1000.0        ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps          = 0             ; Maximum number of (minimization) steps to
perform
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist         = 1             ; Frequency to update the neighbor list and
long range forces
ns_type         = simple                ; Method to determine neighbor list
(simple, grid)
rlist           = 9.0           ; Cut-off for making neighbor list (short
range forces)
coulombtype     = Cut-off               ; Treatment of long range
electrostatic interactions
rcoulomb        = 9.0           ; Short-range electrostatic cut-off
rvdw            = 9.0           ; Short-range Van der Waals cut-off
pbc             = no            ; Periodic Boundary Conditions (yes/no)
/


*If I used this mdp file for 0-step minimization, I could get potential
energy around 700 kJ/mol for my system. But I would get potential energy
around 2.6e+05 kJ/mol if I used the mdv.mdp (md simulation in vacuum) for
calculations with rerun option. And the bond potential could also reach as
high as 1.1e+05 kJ/mol. Actually, my system is very small, it contains only
37 atoms. I believe that the energy reported by 0-step minimization were
more reasonable. So I guess that there might be some problem for the mdp
file usd with rerun, and here is the mdv.mdp:*



/define              = ;-DPOSRES 
integrator          =  md       ; molecular dynamics algorithm
tinit               =  0.0      ; start time and timestep in ps
dt                  =  0.002    ; time step in ps
nsteps              =  2        ; number of steps for 1000ns run
emtol               =  100    ; convergence criterion
emstep              =  0.05      ; intial step size
nstlist             =  0       ; step frequency for updating neighbour list
ns_type             =  simple     ; method for neighbour searching (?)
nstxout             =  1    ; frequency for writing coords to output .trr
file
nstvout             =  1     ; frequency for writing velocities to
output...should be same as nstxout
nstfout             =  1        ; frequency for writing forces to output
nstlog              =  1      ; frequency for writing energies to log file
nstenergy           =  1      ; frequency for writing energies to energy
file
nstxtcout           =  1     ; 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               =  0      ; cutoff lengths (nm)
epsilon_r           =  1.0      ; Dielectric constant (DC) for twin-range or
DC of reaction field
niter               =  100      ; Some thingies for future use 
fourierspacing      =  0.16
fourier_nx          =  30
fourier_ny          =  30
fourier_nz          =  30
coulombtype         =  Cut-off      ; truncation for minimisation, with
large cutoff
rcoulomb            =  0
rcoulomb-switch     =  0
vdw-type                 = Cut-off  ; truncation for minimisation, with
large cutoff
rvdw-switch              = 0
rvdw                     = 0   ; cut-off lengths
epsilon_surface          = 0
optimize_fft             = yes
Tcoupl              =  V-rescale
tc_grps             = system 
tau_t               = 0.01 
ref_t               = 300
Pcoupl              = no ; Parrinello-Rahman ; Pressure coupling    
gen_vel             =  yes
gen_temp            =  300
gen_seed            =  -1
constraints         = none  ; OPTIONS FOR BOND CONSTRAINTS 
constraint-algorithm  = Lincs   ; Type of constraint algorithm
lincs_order         =  4        ;4        ; Highest order in the expansion
of the constraint coupling matrix
lincs_iter          =  1
lincs_warnangle     =  30       ; Lincs will write a warning to the stderr
if in one step a bond rotates 
                                ; over more degrees than 
unconstrained-start      = no   ; Do not constrain the start configuration
;Shake-SOR                = no   ; Use successive overrelaxation to reduce
the number of shake iterations
;shake-tol                = 1e-04 ; Relative tolerance of shake
morse                    = no   ; Convert harmonic bonds to morse potentials
/


*Could you please have a check for me again? Thanks in advance!

All the best,
Qinghua*


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