[gmx-users] gromacs.org_gmx-users Digest, Vol 150, Issue 114

[张慧玲]

Billy and Justin，thank you. I will try that.
Hui 


> -----原始邮件-----
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> 发送时间: 2016年10月27日 星期四
> 收件人: gromacs.org_gmx-users at maillist.sys.kth.se
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> 主题: gromacs.org_gmx-users Digest, Vol 150, Issue 114
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> Today's Topics:
> 
>    1. Re: HELP?how could the simulation restarted from md*_prev.cpt
>       rather than the md*.cpt (Billy Williams-Noonan)
>    2. Re: HELP?how could the simulation restarted from md*_prev.cpt
>       rather than the md*.cpt (Billy Williams-Noonan)
>    3. Re: HELP?how could the simulation restarted from md*_prev.cpt
>       rather than the md*.cpt (Justin Lemkul)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 27 Oct 2016 16:43:01 +1100
> From: Billy Williams-Noonan <billy.williams-noonan at monash.edu>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] HELP?how could the simulation restarted from
>  md*_prev.cpt rather than the md*.cpt
> Message-ID:
>  <CABYyyNGMGUszVLDA5GPtb4O=nXLegrKuRNe5PR1xH=_ujXc=Cg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Howdy,
> 
> I'm no expert on this topic, but from a file processing standpoint, I would
> just move all your current md*.cpt files into a new directory and write a
> quick script to rename your md*_prev.cpt files to md*.cpt files in the
> current directory.
> 
> Cheers,
> 
> Billy
> 
> On Thursday, 27 October 2016, ??? <hl.zhang at siat.ac.cn> wrote:
> 
> > Hi?
> >     I have 17 replicas for a simulation, and Gromacs outputs two cpt files
> > for each replica: md*_prev.cpt and md*.cpt
> >     I know I can restart the simulation from checkpoint using the command
> > "mpirun -np 17 mdrun-deffnm md -multi 17 -noddcheck -replex 50000 -nsteps
> > 100000000 -cpi md", but how could I restart the simulatio from md*_prev.cpt
> > rather than the md*.cpt?
> >     Thanks a lot for your help.
> >
> >
> > Hui
> >
> >
> >
> >
> >
> >
> > --
> > Gromacs Users mailing list
> >
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> 
> 
> -- 
> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
> 
> *LinkedIn Profile
> <http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
> **|*   +61420 382 557
> 
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 27 Oct 2016 19:51:06 +1100
> From: Billy Williams-Noonan <billy.williams-noonan at monash.edu>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] HELP?how could the simulation restarted from
>  md*_prev.cpt rather than the md*.cpt
> Message-ID:
>  <CABYyyNH5AaU5AKSjK0vTDOrdPtVw7qHz2JzWvxYy5NUWeBKhDA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Try this Perl script.
> 
> 
> for $i (x..y) {
>    system "mv md${i}_prev.cpt md${i}.cpt" ;
> 
> }
> 
> 
> Billy
> 
> 
> On Thursday, 27 October 2016, Billy Williams-Noonan <
> billy.williams-noonan at monash.edu> wrote:
> 
> > Howdy,
> >
> > I'm no expert on this topic, but from a file processing standpoint, I
> > would just move all your current md*.cpt files into a new directory and
> > write a quick script to rename your md*_prev.cpt files to md*.cpt files in
> > the current directory.
> >
> > Cheers,
> >
> > Billy
> >
> > On Thursday, 27 October 2016, ??? <hl.zhang at siat.ac.cn
> > <javascript:_e(%7B%7D,'cvml','hl.zhang at siat.ac.cn');>> wrote:
> >
> >> Hi?
> >>     I have 17 replicas for a simulation, and Gromacs outputs two cpt
> >> files for each replica: md*_prev.cpt and md*.cpt
> >>     I know I can restart the simulation from checkpoint using the command
> >> "mpirun -np 17 mdrun-deffnm md -multi 17 -noddcheck -replex 50000 -nsteps
> >> 100000000 -cpi md", but how could I restart the simulatio from md*_prev.cpt
> >> rather than the md*.cpt?
> >>     Thanks a lot for your help.
> >>
> >>
> >> Hui
> >>
> >>
> >>
> >>
> >>
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support
> >> /Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >
> >
> >
> > --
> > Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
> >
> > *LinkedIn Profile
> > <http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
> > **|*   +61420 382 557
> >
> > Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> > Royal Parade, Parkville, 3052
> >
> >
> >
> 
> -- 
> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
> 
> *LinkedIn Profile
> <http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button>
> **|*   +61420 382 557
> 
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Thu, 27 Oct 2016 05:47:56 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] HELP?how could the simulation restarted from
>  md*_prev.cpt rather than the md*.cpt
> Message-ID: <df369bfc-9f85-656f-990e-287654718cd4 at vt.edu>
> Content-Type: text/plain; charset=gbk; format=flowed
> 
> 
> 
> On 10/26/16 11:05 PM, ??? wrote:
> > Hi?
> >     I have 17 replicas for a simulation, and Gromacs outputs two cpt files for each replica: md*_prev.cpt and md*.cpt
> >     I know I can restart the simulation from checkpoint using the command "mpirun -np 17 mdrun-deffnm md -multi 17 -noddcheck -replex 50000 -nsteps 100000000 -cpi md", but how could I restart the simulatio from md*_prev.cpt rather than the md*.cpt?
> >     Thanks a lot for your help.
> >
> 
> Tell mdrun to do that with -cpi md_prev.cpt instead of what you're doing now, 
> which is -cpi md.cpt
> 
> -Justin
> 
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==================================================
> 
> 
> ------------------------------
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> End of gromacs.org_gmx-users Digest, Vol 150, Issue 114
> *******************************************************