[gmx-users] Re: Fast exchanges for REMD

[Michael Shirts]

> However, the time value (4 in this example) is limited to 6 digits.

Sounds like this should be increased?  There's a pending change to
replica exchange, so this could be added to 4.6 without disrupting the
release timing.

On Wed, Sep 26, 2012 at 11:22 AM, Andreas Zink <zinkandi at googlemail.com> wrote:
> Dear all,
>
> I could finally demux my REMD trajectories with high EAF. They look fine,
> but I'm not 100% sure about it.
>
> Unfortunately, there seems to be a "bug" in mdrun. As you migh know, the log
> files contain the exchange attempts like:
>>
>> Replica exchange at step 2000 time 4
>> Repl ex  0    1    2    3 x  4    5
>> Repl pr        .00       1.0
>
> However, the time value (4 in this example) is limited to 6 digits. It's not
> really a bug because I think GROMACS recommends EAFs of max. 1/ps. But if
> you exchange every 0.5 ps (EAF= 2/ps) you can run the simulation for max.
> 99999 ps only. Otherwise your log will simply chop the time after the
> decimal point, e.g.
>
>> Replica exchange at step ... time 99999.5
>> ...
>>
>> Replica exchange at step ... time 100000
>> ...
>>
>> Replica exchange at step ... time 100000
>> ...
>>
>> Replica exchange at step ... time 100001
>> ...
>
> I have written a Perl script which fixes the time values, based on the given
> number of steps and stepsize. Additionally the demux.pl script was changed
> because it also chops after 6 digits. I simply changed:
>>
>> printf(NDX "%-20g",$t);
>
> in the "pr_order" and "pr_revorder" subroutines to:
>>
>> printf(NDX "%-20.2f",$t);
>
> and it works just fine.
>
> Like I said the trajectories look fine, but I'm not really sure if it's
> actually correct that way. I would be happy if anyone would like to discuss
> this :)
>
>
> Cheers,
>
> Andi
>
>
>
>
> Am 24.09.2012 08:49, schrieb Andreas Zink:
>
>> Dear all,
>>
>> I've done some REMD simulations using a quite high exchange attempt
>> frequency (10 attempts per ps) as proposed by Sindhikara et al. ("Exchange
>> Often and Properly in Replica Exchange Molecular Dynamics",J. Chem. Theory
>> Comput. 2010, 6, 2804–2808 ).
>> Unfortunately, I have now recognized that the demux perl script cannot
>> account for an EAF which is higher than the saving frequency in the
>> trajectory.
>>
>> Comments from demux.pl:
>> # If your exchange was every N ps and you saved every M ps you can make
>> for
>> # the missing frames by setting extra to (N/M - 1). If N/M is not integer,
>> # you're out of luck and you will not be able to demux your trajectories
>> at all.
>>
>> In my case exchanges every 0.1 ps and saved every 5 ps
>>
>> Changing the demux.pl script, so that it writes the "replica_index.xvg"
>> with a higher precision (time in ps) should be no problem. However, my
>> question is: will this work together with trjcat? Does trjcat search for the
>> timeframe given in the first column of "replica_index.xvg", or does it links
>> each line to one saved timeframe? If so, could I just delete the additional
>> lines in "replica_index.xvg"?
>>
>> I would be really happy if someone could help me with this!
>> Thanks!
>>
>> Andi
>>
>
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