Dear Sir,
Thank you for the advice. I have not understood the things properly,
especially the convergence of REMD. I got two relevant papers : 1. Convergence
of replica exchange molecular dynamics
2. Convergence and sampling efficiency in replica exchange simulations of
peptide folding in explici
Hi to everybody,
Bharat, maybe i didn't follow exactly the wole tale, but is it possible you
are running xmgrace without the -nxy option?
You are probably visualizing the data related the 1st replica several times!
Francesco
2013/5/24 Mark Abraham
> On Fri, May 24, 2013 at 10:44 AM, bharat gup
On Fri, May 24, 2013 at 10:44 AM, bharat gupta wrote:
> Dear Sir,
>
> Thank you for your detailed response to my query. I understood the concept
> of ordered arrangement of ensembles in replica_index.xvg. But I have a
> doubt, you said that " *At time 4, replicas in ensemble 1 and 2 have
> exchang
Dear Sir,
Thank you for your detailed response to my query. I understood the concept
of ordered arrangement of ensembles in replica_index.xvg. But I have a
doubt, you said that " *At time 4, replicas in ensemble 1 and 2 have
exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in
At time 0 we have an set of replicas and an (ordered) set of ensembles. We
could label these however we liked, but for (in)convenience we use 0-(n-1)
for both. The rows of the matrices in the *.xvg files change with time. At
time 2, replicas in ensemble 0 and 1 have exchanged, so replica 0 is now i
Dear Sir,
I tried a lot to understand the meaning and relation between the .log file
and relica_index file, but I was not able to break the code. I tried to
look into gmx forum for some clue, but didn't find any. So, if possible can
you explain it ...
Replica exchange at step 1000 time 2
Repl 0 <
Looked fine
On Thu, May 23, 2013 at 4:13 PM, bharat gupta wrote:
> Sir,
>
> What about the description of replica_temp file that I posted in last mail.
> I think that's correct ... If you can comment on that, I can move on with
> replica_index file...
>
>
> On Thu, May 23, 2013 at 10:58 PM, Mark
Sir,
What about the description of replica_temp file that I posted in last mail.
I think that's correct ... If you can comment on that, I can move on with
replica_index file...
On Thu, May 23, 2013 at 10:58 PM, Mark Abraham wrote:
> It's a demux. One might want trajectories to be at constant te
It's a demux. One might want trajectories to be at constant temperature, or
constant replica. The two files define the (mutually inverse) mappings
between those representations. So one file tells you which replica is at
each temperature, and the other which temperature holds each replica.
Nobody's
I checked the md.log and replica_temp.xvg file , what I understood is that
the 'x' means swapping and replica are written this way.
For eg.
Replica exchange at step 1000 time 2
Repl 0 <-> 1 dE = -1.067e+00
Repl ex 0 x 123456789 10 11 12 x 13
Repl pr 1.0
Dear Sir,
I checked the md.log and replica_temp.xvg file , what I understood is that
the 'x' means swapping and replica are written this way.
For eg.
Replica exchange at step 1000 time 2
Repl 0 <-> 1 dE = -1.067e+00
Repl ex 0 x 123456789 10 11 12 x 13
Repl
Dear Sir,
I checked the md.log and replica_temp.xvg file , what I understood is that
the 'x' means swapping and replica are written that way.
For eg.
Replica exchange at step 1000 time 2
Repl 0 <-> 1 dE = -1.067e+00
Repl ex 0 x 123456789 10 11 12 x 13
Repl
Each md.log has all the information about all replica exchanges, as you can
see. I suggested you look at your .log and .xvg files a week ago ;-)
There's no problem if a script post-processes all the identical information
from each .log file.
Mark
On Thu, May 23, 2013 at 9:01 AM, bharat gupta wro
I checked the first 5 md.log files, and the data is exactly the same in all
of them Does it mean there could be problem with demux.pl
On Thu, May 23, 2013 at 3:53 PM, Mark Abraham wrote:
> Look at those files. Use diff. They're all the same. Your plots are
> probably all showing the first c
Look at those files. Use diff. They're all the same. Your plots are
probably all showing the first column of each. You want to look at each
column. (And even then the best it can show is that your simulation is not
clearly inadequate.)
Mark
On Thu, May 23, 2013 at 8:48 AM, bharat gupta wrote:
>
Dear Sir,
Thank you for your reply. But I used the command demux.pl md$.log , where
$= No. of replica. I get the same plot every time. Sorry to ask this , but
where am I going wrong ??
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* Please
On Wed, May 22, 2013 at 2:19 AM, bharat gupta wrote:
> Dear Sir,
>
> I performed another round of trial with different set of temperature and I
> got the avg accp. ration around 0.22. Here's the temp. dist. that I used :
> 250 268 288 308 331 355 380 408 438 469 503 540 579 621
>
> I then checked
Dear Sir,
I performed another round of trial with different set of temperature and I
got the avg accp. ration around 0.22. Here's the temp. dist. that I used :
250 268 288 308 331 355 380 408 438 469 503 540 579 621
I then checked the replica_index and replica_temp files for each replica
individu
Dear Sir,
I performed another round of trial with different set of temperature and I
got the avg accp. ration around 0.22. Here's the temp. dist. that I used :
250 268 288 308 331 355 380 408 438 469 503 540 579 621
I then checked the replica_index and replica_temp files for each replica
individu
On Sat, May 18, 2013 at 5:17 PM, bharat gupta wrote:
> Dear Sir,
>
> My main objective of carrying out REMD is to study peptide folding and if
> possible to get some insight in protein design and folding. I read some
> articles related to my work and they always show temp (replica_index)
> graphs
Dear Sir,
My main objective of carrying out REMD is to study peptide folding and if
possible to get some insight in protein design and folding. I read some
articles related to my work and they always show temp (replica_index)
graphs for 2-3 replicas , saying that the sufficient sampling had been
a
On Fri, May 17, 2013 at 4:26 PM, bharat gupta wrote:
> Dear Sir,
>
> The the default bin width is 0.1 which I used for plotting the graphs.
>
That's nice. You need to decide what you need to do about it if you want
graphs that look like those you see reported :-)
> Another question is about you
Dear Sir,
The the default bin width is 0.1 which I used for plotting the graphs.
Another question is about your last reply to my thread "exchange acceptance
is a poor proxy for sampling efficiency". Sorry to ask this, but how to
check whether the sampling efficiency is optimal or not (what should
Histograms 101: The smaller your bin width, the more variations you see.
The more samples you have, the fewer variations you see. A histogram that
does not mention either of this is a work of fiction.
The number of degrees of freedom in the potential energy distribution is
also a factor in whether
What do you not like in your distributions? What are your looking for in these
distributions?
I am not sure what you are expecting from the list here … your distributions
are fine, but, as Mark noted, it does not mean your simulation and sampling
will be optimal …
On May 17, 2013, at 3:51 P
Dear Sir,
I tried plotting the PE overlap using the following way :-
1. extract PE of each replica using g_energy
2. get the PE distribution using g_analyze -f potential_0.xvg -dist pot0.xvg
3. used xmgrace to plot all the PE distribution graphs together.
The same thing I did for temperature dis
Well use a regular plotting software and look at it or do some more elaborated
operation in or out the software to estimate the overlap :))
On May 17, 2013, at 1:14 PM, bharat gupta wrote:
> Dear Sir,
>
> I ran the REMD simulation with temp. distribution discussed in my last
> thread. Each re
Dear Sir,
I ran the REMD simulation with temp. distribution discussed in my last
thread. Each replica was run for 50 ns
Replica exchange statistics
Repl 24999 attempts, 12500 odd, 12499 even
Repl average probabilities:
Repl 0123456789 10 11 12
Repl
Dear gmx members,
I performed a REMD simulation on a peptide 384 atoms (24 residues). In
total 11 replicas were simulated for a period of 50ns each. The exchange
was allwoed at every 1000 steps. The output of md.log file is :
Replica exchange statistics
Repl 24999 attempts, 12500 odd, 12499 even
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