Hi Dan,
Thank you very much. I follow the manual and command the you have referred. But I got the following error during processing my rem log file. It is not generating the output file 'accept.dat'. Please suggest what to do.
CPPTRAJ: Trajectory Analysis. V14.25
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
> readdata test-rem.log as remlog
Reading 'test-rem.log' as Amber REM log with name 'test-rem.log'
Reading from log files: test-rem.log
32 Hamiltonian replicas.
Initial H-REMD coordinate indices: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
test-rem.log should contain 340 exchanges
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
<runanalysis remlog test-rem.log out trepidx.agr repidx name acceptout accept.dat
REMLOG: test-rem.log, 32 replicas, 340 exchanges
Getting replica index vs exchange.
Output is to trepidx.agr
Error: [remlog] Not all arguments handled: [ acceptout accept.dat ]
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
TIME: Total analysis execution time: 0.0070 seconds.
> -----Original Messages-----
> From: "Daniel Roe" <daniel.r.roe.gmail.com>
> Sent Time: 2017-12-19 02:50:19 (Tuesday)
> To: "AMBER Mailing List" <amber.ambermd.org>
> Cc:
> Subject: Re: [AMBER] HREMD run
>
> See the Amber 17 manual, 28.10.25. remlog (page 670-671) for command
> syntax, details, and examples.
>
> -Dan
>
> On Mon, Dec 18, 2017 at 6:28 AM, Dr. MANAS MONDAL <manas.pku.edu.cn> wrote:
> >
> > What is the syntax for 'remlog' analysis command in cpptraj and how I will run it using my rem.log file ?
> >
> > Manas
> >
> >> -----Original Messages-----
> >> From: "Daniel Roe" <daniel.r.roe.gmail.com>
> >> Sent Time: 2017-12-15 22:38:10 (Friday)
> >> To: "AMBER Mailing List" <amber.ambermd.org>
> >> Cc:
> >> Subject: Re: [AMBER] HREMD run
> >>
> >> Hi,
> >>
> >> Exchange acceptance is printed in the HREMD log, the very last column.
> >>
> >> You can also use the 'remlog' analysis command from cpptraj to
> >> calculate the exchange acceptance from 1 or more rem logs.
> >>
> >> -Dan
> >>
> >>
> >> On Thu, Dec 14, 2017 at 8:47 PM, Dr. MANAS MONDAL <manas.pku.edu.cn> wrote:
> >> > Hi,
> >> > Please let me help by giving me the information about how can I calculate the Exchange acceptance ratio from the output log file (rem.log) of the HREMD run. I am waiting for your response.
> >> > Thanking you.
> >> > Manas
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe
> >> Laboratory of Computational Biology
> >> National Institutes of Health, NHLBI
> >> 5635 Fishers Ln, Rm T900
> >> Rockville MD, 20852
> >> https://www.lobos.nih.gov/lcb
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Dec 18 2017 - 19:00:03 PST
