to the end of the command you typed add: -deffnm cbd211_md
Em sáb, 17 de nov de 2018 às 08:00, <gromacs.org_gmx-users-request@maillist. sys.kth.se> escreveu: > 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: Recovery simulation error (Bratin Kumar Das) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 17 Nov 2018 09:33:24 +0530 > From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Recovery simulation error > Message-ID: > < > cam7tw5tjyoudjqapcgeb6odi58vh-2q_-ymstzoteng_asp...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Use the following command... > Gmx mdrun -v -s cbd211_md.tpr -cpi cbd211_md.cpt -append -deffnm cbd211_md > > On Sat, Nov 17, 2018, 9:26 AM Bratin Kumar Das < > 177cy500.bra...@nitk.edu.in> > wrote: > > > Use -deffnm flag and specify the name ..same as the previous output > > file...do not forget to give the -append flag > > > > On Sat, Nov 17, 2018, 3:09 AM Mario Andres Rodriguez Pineda < > > mand...@iq.usp.br> wrote: > > > >> Hi Gromacs Users. > >> I has been a simulation with gromacs 2016 but my simulation stopped by > an > >> energy break. i try to restar in the last checkpoint but this does work > >> and > >> send me this error: > >> Expected output files not present or named differently: > >> cbd211_md.log > >> cbd211_md.xtc > >> cbd211_md.trr > >> cbd211_md.edr > >> Fatal error: > >> File appending requested, but 4 of the 4 output files are not present or > >> are > >> named differently. For safety reasons, GROMACS-2016 and later only > allows > >> file > >> appending to be used when all files have the same names as they had in > the > >> original run. Checkpointing is merely intended for plain continuation of > >> runs. > >> For safety reasons you must specify all file names (e.g. with -deffnm), > >> and > >> all these files must match the names used in the run prior to > >> checkpointing > >> since we will append to them by default. If the files are not available, > >> you > >> can add the -noappend flag to mdrun and write separate new parts. For > mere > >> concatenation of files, you should use the gmx trjcat tool instead. > >> > >> I used this command: > >> gmx mdrun -s cbd211_md.tpr -cpi cbd211_md.cpt -v > >> > >> All the archives ar in the directory.... > >> > >> Can you help me? Thanks > >> > >> > >> > >> -- > >> *MSc. MARIO ANDR?S RODR?GUEZ PINEDA* > >> *Estudiante Doctorado en Biotecnolog?a* > >> *UNAL- MEDELL?N * > >> -- > >> 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. > > > > > > > ------------------------------ > > -- > 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 175, Issue 60 > ****************************************************** > -- 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.