[gmx-users] g_msd, REMD, trestart...

Julián GC jgelcon at yahoo.com.ar
Sat Mar 15 21:54:35 CET 2008

Thanks for your help, Mark.

I cannot demux the trajectories, because I'm running each box at with a different temperature
and with a different initial configuration (appropiate to that temperature)
(This, combined with the replica exchange, is usually called "parallel tempering").

Checking the g_msd -h I saw that I can save some time using g_msd -e and -b (end and begin 
time for the MSD measurement), but that's the best I can see right now.

I do see the discontinuities you mention, thats what I would like to avoid. And, I agree: if I 
realize I need statistics on blocks longer than 100ps, I'm gonna have to try something else,
at least reducing the replica exchange frequency

Thanks again, bye,


Mark Wrote:

>Julián GC wrote:
>> Hi all,
>> I'm studying small water clusters with Gromacs 3.3 (I'm also performing 
>> MC with a self-writed MC program).
>> I run 24 boxes in paralell, with -replex 100000 (it is important to use 
>> replica exchange).
>> I need to get MSD results, but I don't think g_msd takes into account 
>> that every 100ps the boxes are being exchanged.

>Constant-T REMD trajectories are intrinsically discontinuous, so g_msd 
>will also have discontinuities. If all of your replicas started from the 
>same structure, then the MSD calculation is measuring from the same 
>starting point. If you need statistics for longer continuous chunks, 
>then you need to reconsider your approach. If you can adjust suitably 
>for temperature, then generating demux-ed constant-replica REMD 
>trajectories will at least eliminate the discontinuities. (demux.pl is 
>either in the source distribution or on the contributions section of the 
>GROMACS webpage, I forget which)

>> Does anyone knows how to fix that? Have anyone had to deal with 
>> something like this before?
>> (The obvious "easy" solution is to chop the trajectory in blocks of 
>> 100ps, calculate MSD in each block, and then average all the results, 
>> but would be nice if this annoying "shortcut" could be avoided)

>See g_msd -h... I think -trestart saves you some legwork here.


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