<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div><pre>Thanks for your help, Mark.<br><br>I cannot demux the trajectories, because I'm running each box at with a different temperature<br>and with a different initial configuration (appropiate to that temperature)<br>(This, combined with the replica exchange, is usually called "parallel tempering").<br><br>Checking the g_msd -h I saw that I can save some time using g_msd -e and -b (end and begin <br>time for the MSD measurement), but that's the best I can see right now.<br><br>I do see the discontinuities you mention, thats what I would like to avoid. And, I agree: if I <br>realize I need statistics on blocks longer than 100ps, I'm gonna have to try something else,<br>at least reducing the replica exchange frequency<br><br>Thanks again, bye,<br><br>Julian<br><br>Mark Wrote:<br><br>>Julián
GC wrote:<br>>><i> <br></i>>><i> <br></i>>><i> Hi all,<br></i>>><i> <br></i>>><i> I'm studying small water clusters with Gromacs 3.3 (I'm also performing <br></i>>><i> MC with a self-writed MC program).<br></i>>><i> I run 24 boxes in paralell, with -replex 100000 (it is important to use <br></i>>><i> replica exchange).<br></i>>><i> <br></i>>><i> I need to get MSD results, but I don't think g_msd takes into account <br></i>>><i> that every 100ps the boxes are being exchanged.<br></i><br>>Constant-T REMD trajectories are intrinsically discontinuous, so g_msd <br>>will also have discontinuities. If all of your replicas started from the <br>>same structure, then the MSD calculation is measuring from the same <br>>starting point. If you need statistics for longer continuous chunks, <br>>then you need to reconsider your approach. If you can adjust suitably <br>>for
temperature, then generating demux-ed constant-replica REMD <br>>trajectories will at least eliminate the discontinuities. (demux.pl is <br>>either in the source distribution or on the contributions section of the <br>>GROMACS webpage, I forget which)<br><br>>><i> Does anyone knows how to fix that? Have anyone had to deal with <br></i>><i>> something like this before?<br></i>>><i> (The obvious "easy" solution is to chop the trajectory in blocks of <br></i>><i>> 100ps, calculate MSD in each block, and then average all the results, <br></i>>><i> but would be nice if this annoying "shortcut" could be avoided)<br></i><br>>See g_msd -h... I think -trestart saves you some legwork here.<br><br>>Mark</pre></div></div><br>
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