# [gmx-users] freezing atom group speed up issue

Sung-Joo Lee sungjoo at stanford.edu
Wed Jul 14 21:59:55 CEST 2004

```Hi,

I've been observing the speed up gained by freezing atoms for my 120k
atom system (20k solvent, 100k protein cage surrounding solvent)

Freezing the protein cage (100k out of 120k) had things moving twice as
fast.. slower than I was hoping it to be.

Basically the freeze group setting killed most of the LJ(T) + Coul(T),
(T=Tabulated), and half of Innerloop-Iatom, and some of Coulomb(T) but
the rest (NS-pairs, RB-Dihedrals, Angles) remain the same.

.mdp setting related to the freezing was. (Dummy is a single atom group,
and Cage consists ~100k atoms)

freezegrps = Dummy Cage
freezedim  = Y Y Y Y Y Y
energygrp_excl = Cage Cage
energygrps      = Cage

Am I missing something here?

Perhaps I could comb through the topology to remove the bonded
interactions within the freeze group

Any suggestions on how to get it even faster?

Thanks,

Sungjoo Lee

Postdoc, Stanford University.
http://folding.stanford.edu

Details follows

None of 120k atoms freezed

RF=Reaction-field  Free=Free Energy  SC=Softcore
T=Tabulated        S=Solvent         W=Water     WW=Water-Water

Computing:      M-Number      M-Flop's  % Flop's
LJ + Coulomb    261.486225   9936.476550     0.7
Coulomb(T)   1100.638222  45126.167102     3.0
Coulomb(T)(W)      7.352676    904.379148     0.1
LJ(T) + Coul(T)  16085.385060  1077720.799020    71.3
LJ(T) + Coul(T)(W)    435.516667  64891.983383     4.3
LJ(T) + Coul(T)(WW)    319.692207  123401.191902     8.2
Innerloop-Iatom    259.895420   2598.954200     0.2
NS-Pairs   4145.122210  87047.566410     5.8
Reset In Box     12.069096    108.621864     0.0
Shift-X    239.228990   1435.373940     0.1
CG-CoM     10.711656    310.638024     0.0
Bonds     50.620570   2176.684510     0.1
Angles    181.145965  29526.792295     2.0
Propers     19.756737   4524.292773     0.3
RB-Dihedrals    169.872703  41958.557641     2.8
Virial    119.642523   2153.565414     0.1
Update    119.615496   3708.080376     0.2
Stop-CM    119.496000   1194.960000     0.1
Calc-Ekin    119.734992   3232.844784     0.2
Lincs     49.732752   2983.965120     0.2
Lincs-Mat    265.790988   1063.163952     0.1
Shake-V    119.615496   1794.232440     0.1
Shake-Vir    119.615496   2153.078928     0.1
Settle      6.740160   2177.071680     0.1
Total                1512129.44146   100.0

NODE (s)   Real (s)      (%)
Time:   1635.680   1636.000    100.0
27:15
(Mnbf/s)   (MFlops) (ps/NODE hour) (NODE hour/ns)
Performance:     13.238    924.465      4.402    227.178

100k of 120k atoms freezed (most protein freezed, and solvent free)

Computing:      M-Number      M-Flop's  % Flop's
LJ + Coulomb    261.486225   9936.476550     2.1
Coulomb(T)    948.149043  38874.110763     8.2
Coulomb(T)(W)      7.476621    919.624383     0.2
LJ(T) + Coul(T)    576.356673  38615.897091     8.1
LJ(T) + Coul(T)(W)    447.212200  66634.617800    14.0
LJ(T) + Coul(T)(WW)    339.711626  131128.687636    27.6
Innerloop-Iatom    136.939390   1369.393900     0.3
NS-Pairs   4166.729882  87501.327522    18.4
Reset In Box     12.069096    108.621864     0.0
Shift-X    239.228990   1435.373940     0.3
CG-CoM     10.711656    310.638024     0.1
Bonds     50.620570   2176.684510     0.5
Angles    181.145965  29526.792295     6.2
Propers     19.756737   4524.292773     1.0
RB-Dihedrals    169.872703  41958.557641     8.8
Virial    119.642523   2153.565414     0.5
Update    119.615496   3708.080376     0.8
Stop-CM    119.496000   1194.960000     0.3
Calc-Ekin    119.734992   3232.844784     0.7
Lincs     49.732752   2983.965120     0.6
Lincs-Mat    265.790988   1063.163952     0.2
Shake-V    119.615496   1794.232440     0.4
Shake-Vir    119.615496   2153.078928     0.5
Settle      6.740160   2177.071680     0.5
Total                475482.05939   100.0

NODE (s)   Real (s)      (%)
Time:    817.810    818.000    100.0
13:37
(Mnbf/s)   (MFlops) (ps/NODE hour) (NODE hour/ns)
Performance:      7.590    581.409      8.804    113.585

```