Re: [gmx-users] Re: REMD average acceptance ratio

2013-05-11 Thread bharat gupta 
Dear Sir,

Thank you for your reply. I choose the temperature distribution using
t-remd calculator. Here's the link for index and temp files .
https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png
https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m.







On Sat, May 11, 2013 at 12:04 AM, XAvier Periole  wrote:

>
> The replicas seem indeed to have exchange. Using a colour for the #
> replicas would help.
>
> I could not access to the first link.
>
> Note also that the increase of exchange ratio with the temperature suggest
> the distribution of the temperature is not optimal and may be with regular
> intervals? You want to use a exponential distribution.
>
> On May 10, 2013, at 4:53 PM, bharat gupta 
> wrote:
>
> > Dear gmx members,
> >
> > I have posted the same question previously , but I didn't get any reply.
> > So, if anyone can help me out ...
> >
> > 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
> > Repl  average probabilities:
> > Repl 0123456789   10
> > Repl  .16  .16  .16  .17  .18  .21  .24  .26  .28  .30
> > Repl  number of exchanges:
> > Repl 0123456789   10
> > Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703
> > Repl  average number of exchanges:
> > Repl 0123456789   10
> > Repl  .16  .16  .17  .17  .17  .21  .24  .26  .28  .30
> >
> > The acceptance ratio for each replica and average acceptance ratio is as
> > calculated below :-
> >
> >accp. ratio
> > 2038 0.16304
> > 2007 0.16056
> > 2065 0.1652
> > 2117 0.16936
> > 2182 0.17456
> > 2587 0.20696
> > 3022 0.24176
> > 3213 0.25704
> > 3554 0.28432
> > 3703 0.29624
> > 0.211904 (avg accp ratio) (Is this value correct ??)
> >
> > The Pdes used while generating temp. range was also 0.2. Does that mean
> > that  replicas have exchanged for the given temp.range ??.  Here's the
> link
> > for both remd_temp and remd_index files (
> > https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png<
> https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png;cid=1368069857486-810
> >)
> > , (
> > https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m<
> https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m&cid=1368069857486-810
> >
> > )
> >
> > --
> > Bharat
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Bharat
Ph.D. Candidate
Biomolecular Engineering Laboratory
Pusan National University
South Korea
Mobile no. - 010-5818-3680
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: REMD average acceptance ratio

2013-05-10 Thread XAvier Periole 

The replicas seem indeed to have exchange. Using a colour for the # replicas 
would help.

I could not access to the first link. 

Note also that the increase of exchange ratio with the temperature suggest the 
distribution of the temperature is not optimal and may be with regular 
intervals? You want to use a exponential distribution.

On May 10, 2013, at 4:53 PM, bharat gupta  wrote:

> Dear gmx members,
> 
> I have posted the same question previously , but I didn't get any reply.
> So, if anyone can help me out ...
> 
> 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
> Repl  average probabilities:
> Repl 0123456789   10
> Repl  .16  .16  .16  .17  .18  .21  .24  .26  .28  .30
> Repl  number of exchanges:
> Repl 0123456789   10
> Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703
> Repl  average number of exchanges:
> Repl 0123456789   10
> Repl  .16  .16  .17  .17  .17  .21  .24  .26  .28  .30
> 
> The acceptance ratio for each replica and average acceptance ratio is as
> calculated below :-
> 
>accp. ratio
> 2038 0.16304
> 2007 0.16056
> 2065 0.1652
> 2117 0.16936
> 2182 0.17456
> 2587 0.20696
> 3022 0.24176
> 3213 0.25704
> 3554 0.28432
> 3703 0.29624
> 0.211904 (avg accp ratio) (Is this value correct ??)
> 
> The Pdes used while generating temp. range was also 0.2. Does that mean
> that  replicas have exchanged for the given temp.range ??.  Here's the link
> for both remd_temp and remd_index files (
> https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png)
> , (
> https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m
> )
> 
> -- 
> Bharat
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: REMD average acceptance ratio

2013-05-10 Thread bharat gupta 
Dear gmx members,

I have posted the same question previously , but I didn't get any reply.
So, if anyone can help me out ...

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
Repl  average probabilities:
Repl 0123456789   10
Repl  .16  .16  .16  .17  .18  .21  .24  .26  .28  .30
Repl  number of exchanges:
Repl 0123456789   10
Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703
Repl  average number of exchanges:
Repl 0123456789   10
Repl  .16  .16  .17  .17  .17  .21  .24  .26  .28  .30

The acceptance ratio for each replica and average acceptance ratio is as
calculated below :-

accp. ratio
2038 0.16304
2007 0.16056
2065 0.1652
2117 0.16936
2182 0.17456
2587 0.20696
3022 0.24176
3213 0.25704
3554 0.28432
3703 0.29624
0.211904 (avg accp ratio) (Is this value correct ??)

The Pdes used while generating temp. range was also 0.2. Does that mean
that  replicas have exchanged for the given temp.range ??.  Here's the link
for both remd_temp and remd_index files (
https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png)
, (
https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m
)

-- 
Bharat
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists