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gromacs做REMD  

2010-12-07 20:21:14|  分类: Gromacs |  标签: |举报 |字号 订阅

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It is pretty simple to set up your MD runs to do REMD.  Make a set of .mdp files, each specifying a different temperature that you wish to use.  Number the output .tpr files according to index, from 0 to whatever (i.e., if you have 10 different temperatures you would have md0.tpr, md1.tpr...md9.tpr).
The interval for replica exchange is given by the mdrun flag -replex (refer to the manual, it's all in there).  The -np flag for mdrun must agree with however many .tpr files you have (i.e., 10 for the above general example using md0.tpr through md9.tpr).  As was explained in a post just a few weeks ago, nomenclature for the input is critical to getting mdrun to work.  Your command line would be:
$grompp -f full0.mdp -c -p -o md0.tpr
...
$grompp -f full9.mdp -c -p -o md9.tpr
$ mdrun -s md.tpr -np 10 -replex (number of steps) (followed by whatever output
options)
That way, mdrun will find all of your md*.tpr files.
Hopefully this helps.  Again, I've only done a few REMD runs, so others may have more details to add.
Note that: this remd technique can be applied only gromacs vesion 3 or successive vesion!
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