I don't know if there is a function in Gromacs that it can get and change a specific group atom's local information,for example data in the t_state data structure , when given a group, which is defined and included by command of grompp -n option. <br>
So I can call this function in the master node and couple severial simulations <font size="-1">simultaneously</font> .<br><br><div class="gmail_quote">2011/3/22 David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">On 2011-03-22 04.42, Mark Abraham wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
On 22/03/2011 2:38 PM, Yukun Wang wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi<br>
What is the function of 'dd_collect_state' used to ?<br>
</blockquote>
<br>
It collects the state of the simulation system, which was distributed<br>
across the parallel nodes, into a single structure.<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
In the md.c there is a function as:<br>
dd_collect_state(cr->dd,state,state_global)<br>
I don't know what' the mean of it,and where was it defined.<br>
<br>
I want to realize a work by gromacs, that there are several<br>
simulations which coulped weakly only by exchanging position<br>
information of a group of atoms for every n steps, and for each<br>
simulation I want to run parallelly. So the trouble is coming for each<br>
simulation with domain decomposition parallelizing that this group of<br>
atoms would be distributed in different node.<br>
How can I get those data from different nodes in the running time? If<br>
I put the self-written coulping code in the master node for each<br>
simulation how I do this data gathering job?<br>
</blockquote>
<br>
Either you need to collect on the master node and communicate between<br>
them before redistributing, or write complex (but ultimately more<br>
scalable) code to communicate between all the processors. The REMD<br>
implementation should be a good model for the former.<br>
<br>
</blockquote></div>
Indeed, or the more general -multi option.<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Mark<br>
</blockquote>
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><div><div></div><div class="h5"><br>
-- <br>
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