[gmx-users] REMD simulation

[Kenny Bravo Rodriguez]

Hi all,

and thanks Mark, Chris and Xavier for your comments.

I finally managed to run the REMD simulation but i can not restart the simulation or continue the simulation after it finished.
I tried with a test system and run two replicas for just 20 ps. After it finished correctly i extended the time in each .tpr file
and tried to continue the REMD simulation using the checkpoint files but i always get the same error message

Multi-checking simulation part ... OK
Multi-checking simulation part ... OK
Reading file test0.tpr, VERSION 4.5.5 (single precision)
Reading file test1.tpr, VERSION 4.5.5 (single precision)
Multi-checking simulation part ... Multi-checking simulation part ... Multi-checking simulation part ... Multi-checking simulation part ... Multi-checking simulation part ... Multi-checking simulation part ... ERROR: 0031-250  task 6: Segmentation fault
ERROR: 0031-250  task 7: Segmentation fault
ERROR: 0031-250  task 2: Segmentation fault
ERROR: 0031-250  task 1: Segmentation fault
ERROR: 0031-250  task 5: Segmentation fault
ERROR: 0031-250  task 3: Segmentation fault
ERROR: 0031-250  task 0: Terminated
ERROR: 0031-250  task 4: Terminated

I used Gromacs 4.5.5 and the following commands:

to start the REMD simulation:
mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500

to extend the time of the simulation in the .tpr files:
tpbconv_d -s test_#.tpr -extend 20 -o test_#.tpr

to continue the REMD simualtion:
mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500

Do i need to use any specific option to be able to continue the REMD simulation?

Thanks in advanced
Kenny






>  Virtual sites also have a hidden benefit - not only can you take a longer
>  time step, but the width of the distribution of PE is relatively wider, so
>  you can have higher exchange probability for the same temperatures.
>
>  Mark
>
>  On Tue, Nov 20, 2012 at 12:34 AM, Christopher Neale<
>  chris.ne... at mail.utoronto.ca>  wrote:
>
>  >  Xavier is right, except that you can also reduce the size of your system.
>  >  You can take larger steps in temperature
>  >  if you have fewer atoms. If you are using a  cubic system, you can move to
>  >  a rhombic dodecahedron.
>  >  Even constraining all bonds will help a bit here (vs. harmonic bonds).
>  >  There are lots of papers on this topic.
>  >
>  >  To see why you don't get any exchanges, construct histograms of your
>  >  potential energies and you will see
>  >  that they don't overlap. Also, it is inefficient to take evenly spaced
>  >  temperatures. This is not your major problem,
>  >  but read a bit on exponentially spaced temperatures for REMD.
>  >
>  >  Chris.
>  >
>  >  -- original message --
>  >
>  >  Well either you use more replicas or you reduce the temperature
>  >  range ...
>  >  There is no way around!
>  >
>  >  On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote:
>  >
>  >  >  Dear All,
>  >  >
>  >  >  i am trying to performed REMD simulations using Gromacs.
>  >  >  My question is concerning the temperature distribution and the
>  >  >  number of replica.
>  >  >  I need to run 24 replicas of my system with a temperature range of
>  >  >  290-400 K. How can I select the temperatures values for each replica?
>  >  >  I tried the serverhttp://folding.bmc.uu.se/remd/index.php  but for
>  >  >  my system it gives 50 replicas. If i try to take 24 evenly spaced
>  >  >  values from the obtained list of temperature then
>  >  >  the replicas do not exchange at all.
>  >  >  I am using Gromacs 4.5.5 and my system has 6862 water molecules and
>  >  >  535 atoms for the solute.
>  >  >
>  >  >  Thanks in advanced
>  >  >  Kenny
>  >  >
>  >  --
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-- 
Kenny Bravo Rodriguez
Max-Planck-Institut für Kohlenforschung
Kaiser-Wilhelm-Platz 1
D-45470 Mülheim an der Ruhr
Germany
Phone: +49 (0)208 306 2160
Email:kenny at mpi-muelheim.mpg.de