Thanks, Mark.<div><br></div><div>Greg<br><br><div class="gmail_quote">On Sat, Nov 13, 2010 at 12:35 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 14/11/2010 4:06 AM, Yongchul Chung wrote:
<blockquote type="cite">Thanks Justin for your prompt reply. I am aware of the
link you provided, but it seems they are rather hand-waving. It
would be nice if I could be directed to a source code of some
sort.</blockquote>
<br></div>
They're "hand-waving" by design of course - a normal user doesn't
care about the details so long as they know how to make it work
right.<br>
<br>
src/gmxlib/checkpoint.c has the details (in 4.5 at least), which
vary quite a bit with MD algorithm and GROMACS version.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">
<div><br>
</div>
<div>Greg<br>
<br>
<div class="gmail_quote">
On Sat, Nov 13, 2010 at 11:50 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
<div><br>
<br>
Yongchul Chung wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
Hello gmx-users,<br>
<br>
I ran two short simulation in series (simulation A
--> simulation B). The output *.gro file from the
simulation A was used as an input file for the
simulation B. If I compare the energy value at the end
of simulation A, and t=0 at simulation B, they are
different (<0.1% deviation). However, if you supply
checkpoint file, you get exactly the same value of the
energy at t=0 for simulation B. I used gmxdump to check
out the contents of cpt file. It seems like the file has
some extra components compared to gro file (which has
position, and velocity information). Several extra
things I found that might be relevant were
'energy_aver', 'energy_sum', and 'energy_n[0]'. It seems
like gromacs somehow use these values internally to
match the energy value at the start of simulation B to
the end of simulation A. <br>
Can someone tell me why there's an error in the energy
value if we don't supply the cpt file, but with cpt
file, there's no error? I suspect it has to do with the
extra information I mentioned above, but not sure where
in the source code to look for more information. <br>
</blockquote>
<br>
</div>
I can't provide any information on the specifics in the
code, but if you think about the purpose and function of the
.cpt file, it makes sense. The .cpt file contains
information about the entire state of the system, which is
described by more than just position and velocities, which,
in the .gro file, are in limited precision.<br>
<br>
For a bit more:<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation" target="_blank">http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation</a><br>
<br>
-Justin
<div>
<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
Thanks,<br>
<br>
Greg<br>
<br>
I'm appending the data, commands, and mdp file below
for the reference.<br>
<br>
// commands<br>
1) Simulation A<br>
grompp -f grompp.mdp -c input_to_A.gro -n index.ndx -p
topol.top<br>
mdrun -s topol.tpr -c output_of_A.gro<br>
<br>
2-1) Simulation B (w/o checkpoint)<br>
grompp -f grompp.mdp -c output_of_A.gro -n index.ndx
-p topol.top<br>
mdrun -s topol.tpr -c output_of_B.gro<br>
<br>
2-2) Simulation B(w/ checkpoint)<br>
grompp -f grompp.mdp -c output of A.gro -n index.ndx
-p topol.top -t state.cpt<br>
mdrun -s topol.tpr -c output_of_B_with_state.gro<br>
<br>
// data<br>
Simulation A energy data<br>
time bond
bond-nc angles
dihedral LJ(SR)
potential kinetic
total energy<br>
0.000000 29233.408203 43995.722656 45702.835938
51693.003906 -144114.109375 26510.859375
85977.609375 112488.468750<br>
0.003000 29246.806641 44015.367188 45684.222656
51694.019531 -144110.906250 26529.500000
85964.890625 112494.390625<br>
0.006000 29247.708984 44022.949219 45585.886719
51695.375000 -144107.500000 26444.421875
86054.156250 112498.578125<br>
0.009000 29241.958984 44016.546875 45426.968750
51697.175781 -144104.265625 26278.390625
86218.250000 112496.640625<br>
0.012000 29235.324219 44005.812500 45257.687500
51699.402344 -144101.031250 26097.203125
86396.218750 112493.421875<br>
0.015000 29231.802734 43999.378906 45130.500000
51701.945312 -144098.000000 25965.625000
86528.429688 112494.054688<br>
0.018000 29231.041016 43994.878906 45067.519531
51704.746094 -144094.390625 25903.796875
86595.398438 112499.195312<br>
0.021000 29227.580078 43988.855469 45058.753906
51707.007812 -144091.468750 25890.718750
86615.390625 112506.109375<br>
0.024000 29213.531250 43979.210938 45072.437500
51708.511719 -144088.968750 25884.718750
86626.640625 112511.359375<br>
0.027000 29182.050781 43970.894531 45074.558594
51708.472656 -144086.500000 25849.468750
86666.546875 112516.015625<br>
0.030000 29130.822266 43963.402344 45045.148438
51706.945312 -144083.968750 25762.343750
86753.906250 112516.250000<br>
<br>
Simulation B energy data (w/o checkpoint supply)<br>
time bond
bond-nc angles
dihedral LJ(SR)
potential kinetic
total energy<br>
0.000000 29177.361328 43958.375000 45142.761719
51717.425781 -144082.890625 25913.031250
86762.046875 112675.078125<br>
0.003000 29105.240234 43942.156250 45086.699219
51714.648438 -144080.843750 25767.906250
86901.765625 112669.671875<br>
0.006000 29024.171875 43924.238281 45048.691406
51711.386719 -144079.562500 25628.921875
87035.437500 112664.359375<br>
0.009000 28946.726562 43907.777344 45057.507812
51707.562500 -144078.187500 25541.375000
87120.882812 112662.257812<br>
0.012000 28883.349609 43891.914062 45115.203125
51703.593750 -144076.875000 25517.187500
87146.593750 112663.781250<br>
0.015000 28838.960938 43876.933594 45194.253906
51698.367188 -144075.921875 25532.578125
87133.734375 112666.312500<br>
0.018000 28811.880859 43862.824219 45258.449219
51691.171875 -144074.359375 25549.968750
87119.765625 112669.734375<br>
0.021000 28797.781250 43848.613281 45278.308594
51680.550781 -144072.375000 25532.875000
87136.203125 112669.078125<br>
0.024000 28790.947266 43837.628906 45248.121094
51666.472656 -144069.750000 25473.421875
87192.453125 112665.875000<br>
0.027000 28788.593750 43833.882812 45184.238281
51649.878906 -144066.250000 25390.343750
87271.281250 112661.625000<br>
0.030000 28791.101562 43838.437500 45111.562500
51631.695312 -144062.437500 25310.359375
87347.335938 112657.695312<br>
<br>
Simulation B energy data (w/ checkpoint supply)<br>
time bond
bond-nc angles
dihedral LJ(SR)
potential kinetic
total energy<br>
0.000000 29130.822266 43963.402344 45045.148438
51706.945312 -144083.968750 25762.343750
86753.906250 112516.250000<br>
0.003000 29062.935547 43950.101562 45003.597656
51704.625000 -144082.593750 25638.671875
86871.796875 112510.468750<br>
0.006000 28987.000000 43933.789062 44987.125000
51702.902344 -144080.546875 25530.265625
86977.445312 112507.710938<br>
0.009000 28915.218750 43915.363281 45016.925781
51700.277344 -144079.140625 25468.640625
87037.531250 112506.171875<br>
0.012000 28857.343750 43895.234375 45089.933594
51697.753906 -144077.906250 25462.359375
87046.164062 112508.523438<br>
0.015000 28817.451172 43875.136719 45177.636719
51693.886719 -144077.312500 25486.796875
87024.257812 112511.054688<br>
0.018000 28794.009766 43857.585938 45244.371094
51687.488281 -144075.656250 25507.796875
87008.031250 112515.828125<br>
0.021000 28782.230469 43840.925781 45260.535156
51677.023438 -144073.578125 25487.140625
87028.789062 112515.929688<br>
0.024000 28777.083984 43828.734375 45221.421875
51662.421875 -144071.265625 25418.390625
87094.679688 112513.070312<br>
0.027000 28775.339844 43824.812500 45144.421875
51644.714844 -144067.640625 25321.656250
87187.125000 112508.781250<br>
0.030000 28777.638672 43829.210938 45058.011719
51625.828125 -144064.296875 25226.390625
87277.976562 112504.367188<br>
<br>
// mdp<br>
<br>
; RUN CONTROL PARAMETERS<br>
integrator = md<br>
; Start time and timestep in ps<br>
tinit = 0.0<br>
dt = 0.003<br>
;nsteps = 10000000<br>
nsteps = 10<br>
; For exact run continuation or redoing part of a run<br>
init_step = 0<br>
; mode for center of mass motion removal<br>
comm-mode = Linear<br>
; number of steps for center of mass motion removal<br>
nstcomm = 100<br>
; group(s) for center of mass motion removal<br>
comm-grps =<br>
<br>
; OUTPUT CONTROL OPTIONS<br>
; Output frequency for coords (x), velocities (v) and
forces (f)<br>
nstxout = 1<br>
nstvout = 1<br>
nstfout = 1<br>
; Checkpointing helps you continue after crashes<br>
nstcheckpoint = 1<br>
; Output frequency for energies to log file and energy
file<br>
nstlog = 1<br>
nstenergy = 1<br>
; Output frequency and precision for xtc file<br>
nstxtcout = xtc_precision =
1000<br>
; This selects the subset of atoms for the xtc file.
You can<br>
; select multiple groups. By default all atoms will be
written.<br>
xtc-grps =<br>
; Selection of energy groups<br>
energygrps = A B<br>
<br>
; NEIGHBORSEARCHING PARAMETERS<br>
; nblist update frequency<br>
nstlist = 1<br>
; ns algorithm (simple or grid)<br>
ns_type = grid<br>
; Periodic boundary conditions: xyz (default), no
(vacuum)<br>
; or full (infinite systems only)<br>
pbc = xyz<br>
; nblist cut-off<br>
rlist = 1.1<br>
;domain-decomposition = no<br>
<br>
; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>
; Temperature coupling<br>
;tcoupl = no<br>
tcoupl = Berendsen<br>
;tcoupl = v-rescale<br>
; Groups to couple separately<br>
tc-grps = system<br>
; Time constant (ps) and reference temperature (K)<br>
tau_t = 0.5<br>
ref_t = 363<br>
; Pressure coupling<br>
Pcoupl = no<br>
;Pcoupl = Berendsen<br>
Pcoupltype = Anisotropic<br>
; Time constant (ps), compressibility (1/bar) and
reference P (bar)<br>
tau_p = 0.33<br>
compressibility = 0 0 0 0 0 0<br>
ref_p = 1.01325 1.01325 1.01325 0 0
0<br>
; Random seed for Andersen thermostat<br>
andersen_seed = -1<br>
<br>
; GENERATE VELOCITIES FOR STARTUP RUN<br>
gen_vel = no<br>
gen_temp = 363<br>
gen_seed = 57597<br>
<br>
</blockquote>
<br>
</div>
</div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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