Billy and Justin,thank you. I will try that. Hui
> -----原始邮件----- > 发件人: gromacs.org_gmx-users-requ...@maillist.sys.kth.se > 发送时间: 2016年10月27日 星期四 > 收件人: gromacs.org_gmx-users@maillist.sys.kth.se > 抄送: > 主题: gromacs.org_gmx-users Digest, Vol 150, Issue 114 > > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > 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-noo...@monash.edu> > To: "gmx-us...@gromacs.org" <gmx-us...@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=c...@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.zh...@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-requ...@gromacs.org <javascript:;>. > > > > -- > 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-noo...@monash.edu> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] HELP?how could the simulation restarted from > md*_prev.cpt rather than the md*.cpt > Message-ID: > <cabyyynh5aau5aksjk0vtdordptvw7qhz2jzwvxyy5nuwebk...@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-noo...@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.zh...@siat.ac.cn > > <javascript:_e(%7B%7D,'cvml','hl.zh...@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-requ...@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 <jalem...@vt.edu> > To: gmx-us...@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-287654718...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > > ------------------------------ > > -- > 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-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 150, Issue 114 > ******************************************************* -- 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-requ...@gromacs.org.