[gmx-users] about my single point calculation

fantasticqhl fantasticqhl at gmail.com
Wed Nov 13 14:10:17 CET 2013


Hello Mark,

I don't get any informing of your reply by e-mail, but get your reply 
searched by google.
Anyway thanks very much for your reply!



Yeah, I used two totally different mdp files for the single point 
calculation because I thought
that gromcs would report the potential energy of my system if I used the 
option -rerun,
no matter what mdp files I used. Gromacs-4.5.5 was used in the calculations.

Some time later, I also tried as you mentioned in the e-mail below. 
Problem was the same.
I used this mdp (attached minim.mdp) file for both 0-step minimization 
and single point calculation with "rerun":
The only difference is the integrator, steep for 0-step minimization 
while md for single point calculation.
And the following lines are the output I got:

Single point calculation with "rerun" :

            Step           Time         Lambda
               0        0.00000        0.00000

    Energies (kJ/mol)
         G96Bond       G96Angle           Improper Dih. LJ-14            
Coulomb-14
     3.97878e+05    1.44370e+04    1.06677e+04    3.93431e+01 9.36593e+01
         LJ (SR)            Coulomb (SR)      Potential Kinetic En.   
      Total Energy
     2.77574e+01    5.17380e+02    4.23661e+05    0.00000e+00 4.23661e+05
     Temperature     Pressure (bar)
     0.00000e+00    0.00000e+00


0-step minimization:

            Step           Time         Lambda
               0        0.00000        0.00000

    Energies (kJ/mol)
         G96Bond         G96Angle        Improper Dih. LJ-14          
Coulomb-14
     5.75700e+01    1.78703e+01    8.25973e-02   -9.22001e+00 5.93500e+01
         LJ (SR)            Coulomb (SR)      Potential Pressure (bar)
    -1.96671e+01    3.75963e+02    4.81949e+02    0.00000e+00


Later, I also used the mdp file which was pasted on the forum (attached 
sp.mdp) to do single point calculation with "rerun",
The following is what I got:

Step           Time         Lambda
               0        0.00000        0.00000

    Energies (kJ/mol)
         G96Bond        G96Angle         Improper Dih. LJ-14           
Coulomb-14
     3.97878e+05    1.44370e+04    1.06677e+04    3.93431e+01 9.36593e+01
         LJ (SR)           Coulomb (SR)      Potential Kinetic En.       
Total Energy
     2.77575e+01    5.17379e+02    4.23661e+05    6.54617e+01 4.23726e+05
   Conserved En.    Temperature      Pressure (bar)
     4.23726e+05    1.45800e+02    0.00000e+00


I found that those energies are pretty much the same as the one 
mentioned above.


The differences between corresponding energies are huge, I still don't 
understand the difference.
My system only contains 37 atom, the energies generated from the 0-step 
minimization seem more
reasonable than those from single point calculation with "rerun".


Do you know the possible reasons which could result in the huge 
difference? Or I made some mistake?
Thanks very much!


All the best,
Qinghua





On Wed, Nov 6, 2013 at 4:07 PM, fantasticqhl <fantastic... at gmail.com> wrote:

> Dear Justin,
>
> I am sorry for the late reply. I still can't figure it out.
>

It isn't rocket science - your two .mdp files describe totally different
model physics. To compare things, change as few things as necessary to
generate the comparison. So use the same input .mdp file for the MD vs EM
single-point comparison, just changing the "integrator" line, and maybe
unconstrained-start (I forget the details). And be aware of
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

Mark

Could you please send me the mdp file which was used for your single point
> calculations.
> I want to do some comparison and then solve the problem.
> Thanks very much!
>
>
> All the best,
> Qinghua
>
> --
> View this message in context:
>http://gromacs.5086.x6.nabble.com/single-point-calculation-with-gromacs-tp5012084p5012295.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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-------------- next part --------------
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 
-------------- next part --------------
; 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)


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