Sir,
I did an remd simulation in implicit solvent for a peptide.I want to
compare the NOE distances from NMR and various conformations from REMD
output. Here how I get various conformations from remd trajectory? .Is any
script is available to find distance between two particular atoms?.How
There's number of analysis tools briefly described in chapter 8 of the
manual, and lots more detail in Appendix D. Have a look at what is
there, and do your background reading of the literature to see the
kinds of things people have done before you.
Mark
On Tue, Jun 25, 2013 at 1:18 PM, Shine A
An acceptance ratio of 0.2/0.3 is normally best. The problem with high
acceptance ratio is that it means that a large portion of the exchanges are
just back and forth exchanges between consecutive exchange and are thus
disturbing the system more that actually helping sampling.
I do not know
Okay Sir, I will try two-three combinations this time and will report back
to you ...
On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote:
An acceptance ratio of 0.2/0.3 is normally best. The problem with high
acceptance ratio is that it means that a large portion of the
You have to convince yourself, not me :)) But I can give you my opinion …
On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote:
Okay Sir, I will try two-three combinations this time and will report back
to you ...
On Thu, May 16, 2013 at 5:25 PM, XAvier Periole
Dear Sir,
Here's the result of three different runs :
Temperature distribution for three trials
Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627
Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611
Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649
md.log
Indeed the Repeat-3 seems good. But I would guess you did not run too long,
right! That would explain the distribution of values!
On May 16, 2013, at 2:04 PM, bharat gupta bharat.85.m...@gmail.com wrote:
Dear Sir,
Here's the result of three different runs :
Temperature distribution for
Okay, now I can start with large production runs .
On Thu, May 16, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote:
Indeed the Repeat-3 seems good. But I would guess you did not run too
long, right! That would explain the distribution of values!
On May 16, 2013, at 2:04 PM, bharat
On Thu, May 16, 2013 at 2:04 PM, bharat gupta bharat.85.m...@gmail.comwrote:
Dear Sir,
Here's the result of three different runs :
Temperature distribution for three trials
Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627
Repeat-2 280 299 319 340 363 388 414 441 471 503
Sorry to ask this simple question but how to read the replica_index and
replica_temp files. I tried to search a lot but didn't find any
information. As I have concatenated all log files and demuxed them. Here's
first 10 lines from both files:-
replica_index:
0 012345
They show which structure is in which ensemble, and the inverse. Look at
the exchange events reported in the .log files and work out which is which.
Mark
On Thu, May 16, 2013 at 5:25 PM, bharat gupta bharat.85.m...@gmail.comwrote:
Sorry to ask this simple question but how to read the
The plots that I showed in my last mail were for all replicas. I tried
plotting the first 500 ps of replica_index and replica_time files. I think
the plots look fine, and there could be problem with the plotting tool .
Here the link for both files ,
The interval between the exchange trial affect the efficiency of REMD but not
the the exchange ratio (at least in principle).
In you case I am not sure what the plot are showing! Are these showing all the
replicas? what are the units?
On May 14, 2013, at 5:07 AM, bharat gupta
Dear Sir,
I repeated the simulation again for 25 replicas with the following temp.
distribution .
280
289.1
298.5
308.2
318.2
328.6
339.3
350.3
361.7
373.5
385.6
398.1
411.1
424.4
438.3
452.5
467.2
482.4
498.1
514.3
531.0
548.3
566.1
584.5
603.5
623.2
The output of md.log file is :-
Replica
You need to increase the temperature gaps indeed if you want acceptance ratio
~0.2/0.3. But again this won't work with the water …
It is not clear what happens in your index file but probably a problem from
grace to plot so many points … you can try to increase the Max drawing path
length in
Dear Sir,
Here's the result for the REMD trial with large temperature gaps.
Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4
447.1 471.0 496.1 522.6 550.5 579.9 610.8
Out of md16.log :
Replica exchange statistics
Repl 249 attempts, 125 odd, 124 even
Repl average
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