[gmx-users] REMD simulation

[Mark Abraham]

That looks very strange. Please file an issue at
redmine.gromacs.orgincluding all your .tpr and .cpt, and assign it to
me.

Mark

On Thu, Dec 13, 2012 at 1:07 PM, Kenny Bravo Rodriguez <
kenny at mpi-muelheim.mpg.de> wrote:

> 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<http://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 <Email%3Akenny at mpi-muelheim.mpg.de>
>
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