[gmx-users] REMD problem
Justin A. Lemkul
jalemkul at vt.edu
Wed Sep 28 23:20:42 CEST 2011
Liu, Liang wrote:
> Yes, they are updated like:
> ...
> Replica exchange at step 5700 time 11.4
> Repl ex 0 1 x 2 3 x 4 5 x 6 7 8 9 x 10 11 x 12
> 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27
> 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x
> 42 43 x 44 45 x 46 47 48 49
> Repl pr 1.0 1.0 1.0 .00 1.0 1.0
> .00 1.0 1.0 1.0 1.0 .00 1.0
> .00 1.0 .00 1.0 .00 .46 .00
> 1.0 .78 1.0 .00
>
> Replica exchange at step 5750 time 11.5
> Repl 0 <-> 1 dE = -7.583e+00
> Repl ex 0 x 1 2 3 4 x 5 6 x 7 8 x 9 10 x 11 12 x
> 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27
> 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41
> 42 x 43 44 45 46 47 48 49
> Repl pr 1.0 .00 1.0 1.0 1.0 1.0
> 1.0 1.0 1.0 1.0 .48 .11 1.0
> .00 1.0 .00 1.0 .00 .00 .01
> 1.0 1.0 .00 .01 .01
>
> Step Time Lambda
> 5800 11.60000 0.00000
>
> Energies (kJ/mol)
> Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 9.69806e+02 1.32207e+03 3.34938e+01 4.93171e+02 -3.91111e+03
> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest.
> 3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+04 0.00000e+00
> Potential Kinetic En. Total Energy Conserved En. Temperature
> -1.78987e+05 4.57462e+04 -1.33240e+05 1.23302e+10 5.62201e+02
> Pres. DC (bar) Pressure (bar) Constr. rmsd
> -2.12803e+02 -5.47109e+02 2.21484e-05
> ...
>
Perhaps someone else can offer an explanation. It should not be possible to run
multiple replicas on a single processor. Also note that your exchange
probability is extremely high; you're likely not obtaining meaningful sampling.
-Justin
> On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Liu, Liang wrote:
>
> Thanks. currently what I see is the program runs very slowly,
> but get .log file for all the 50 replicas, does this mean all of
> them are running?
>
>
> Are the log files being updated, or do they all simply contain a
> fatal error message that there are insufficient nodes? I cannot
> think of a reason why 50 simulations could possibly run on 2 processors.
>
> -Justin
>
> On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Liu, Liang wrote:
>
> Well, although this makes sense, why all the 50 replicas are
> running when I run "mpirun
> -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on
> my own
> computer with only 2 cores?
>
>
> I can offer no explanation for this behavior, but I expect that
> either not all of them are actually running, or at the very least
> you will get horribly slow performance.
>
>
> By the way, would you please show me where I can find the
> reasonable replex number information in the literature?
> I did
> not find it in the link you posted and the manual either.
>
>
> A few minutes of real literature searching will be far more
> valuable
> than some random person on the Internet giving you a value
> that you
> blindly use ;)
>
> -Justin
>
> Thanks.
>
>
> -- Best,
> Liang Liu
>
>
> -- ==============================____==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080 <tel:%28540%29%20231-9080>
> <tel:%28540%29%20231-9080>
>
> http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
> <http://vt.edu/Pages/Personal/justin>
> <http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>
>
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> --
> Best,
> Liang Liu
>
>
> --
> ==============================__==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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> --
> Best,
> Liang Liu
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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