[gmx-users] understanding the output of REMD
sreelakshmi ramesh
sree.lakshmi at research.iiit.ac.in
Thu Jul 28 03:33:33 CEST 2011
demultiplex script was used to gave one log file of one replica as the
input like perl demux.pl md0.log it gave two output files.
replica_index.xvg and replica_temp.xvg.
the file replica_temp looks like this
0 0 1 2 3 4 5 6 7
2 0 1 2 3 4 5 7 6
4 0 1 2 3 4 5 7 6
6 0 1 2 3 5 4 6 7
8 0 1 2 3 5 4 6 7
10 0 1 2 3 5 4 6 7
12 0 1 2 4 5 3 6 7
14 0 1 2 4 5 3 6 7
16 0 1 2 3 5 4 6 7
18 0 1 2 3 5 4 7 6
20 0 1 2 3 5 4 7 6
22 0 1 2 3 5 4 7 6
24 0 1 2 3 5 4 7 6
26 0 1 2 3 5 4 6 7
28 0 1 2 3 5 4 6 7
30 0 1 2 3 5 4 6 7
32 0 1 2 3 5 4 6 7
34 0 1 2 3 5 4 6 7
the other index file was passed over trjcat and i concatenated all the other
trajectories like this
trjcat -f *.trr -demux replica_index.xvg -o final.trr
now how to produce temp evolution over time with these concatenated
trajectories
thanks in advance,
sree.
On Thu, Jul 28, 2011 at 6:53 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> sreelakshmi ramesh wrote:
>
>> after having enough exchanges how to follow the temp trajectory of each
>> replica in REMD ? I tried to make it out from edr file of each replica.looks
>> like replica at a particular temp remains almost at a same temp throughout
>> the simulation and does not visit all the other tempratures.any help please.
>>
>>
>>
> Trajectories and energy files are ensemble-continuous. Use the demux.plscript to demultiplex the trajectories and produce temperature evolution
> over time.
>
> -Justin
>
> Regards,
>> sree.
>>
>>
>> On Wed, Jul 27, 2011 at 4:58 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> sreelakshmi ramesh wrote:
>>
>> dear all ,
>> I am new to ReMD simulations.And i done a trial run of 100 ps
>> for 7 replicas . if i view the log file for output i get
>> something like this for every replica
>> for one of the replica the log file looks like this
>>
>> Replica exchange at step 1000 time 2
>> Repl 0 <-> 1 dE = 6.793e+02 dpV = 0.000e+00 d = 6.793e+02
>> Repl ex 0 1 2 3 4 5 6
>> Repl pr .00 .00 .00 Replica exchange at step
>> 2000 time 4
>> Repl ex 0 1 2 3 4 5 6
>> Repl pr .00 .00 .00
>> Replica exchange at step 3000 time 6
>> Repl 0 <-> 1 dE = 6.790e+02 dpV = 0.000e+00 d = 6.790e+02
>> Repl ex 0 1 2 3 4 5 6
>> Repl pr .00 .00 .00 Replica exchange at step
>> 4000 time 8
>> Repl ex 0 1 2 3 4 5 6
>> Repl pr .00 .00 .00
>> Replica exchange at step 5000 time 10
>> Repl 0 <-> 1 dE = 6.874e+02 dpV = 0.000e+00 d = 6.874e+02
>> Repl ex 0 1 2 3 4 5 6
>> Repl pr .00 .00 .00 Replica exchange at step
>> 6000 time 12
>> Repl ex 0 1 2 3 4 5 6
>> Repl pr .00 .00 .00
>> Replica exchange at step 7000 time 14
>> Repl 0 <-> 1 dE = 6.535e+02 dpV = 0.000e+00 d = 6.535e+02
>> Repl ex 0 1 2 3 4 5 6
>> Repl pr .00 .00 .00 i had attached only
>> few lines of log file.can any one tel me
>> how to understand the output.
>>
>>
>> I assume you've seen the following?
>>
>> http://www.gromacs.org/__**Documentation/How-tos/REMD#__**
>> Understanding_REMD-related___**Output<http://www.gromacs.org/__Documentation/How-tos/REMD#__Understanding_REMD-related___Output>
>> <http://www.gromacs.org/**Documentation/How-tos/REMD#**
>> Understanding_REMD-related_**Output<http://www.gromacs.org/Documentation/How-tos/REMD#Understanding_REMD-related_Output>
>> >
>>
>> Listed are the exchange probabilities between neighboring replicas.
>> Your results indicate that your systems are not exchanging (e.g.
>> probability is zero).
>>
>> -Justin
>>
>> -- ==============================**__==========
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
>> ==============================**__==========
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> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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