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...@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
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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
; 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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