[gmx-users] REMD problem

Liu, Liang liu4gre at gmail.com
Wed Sep 28 23:17:18 CEST 2011


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
...

On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul <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>> 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> | (540) 231-9080
>>    <tel:%28540%29%20231-9080>
>>
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
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>> >
>>
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Best,
Liang Liu
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