Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 28 - start the simulation of the last stopping point.
Hi, Those were not the commands you issued. What commands did you issue? Mark On Fri, Nov 9, 2018 at 7:12 AM Edjan Silva wrote: > Dear Paul, > > Thank you for your help. However, when you run the command: > > $ gmx convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr > $ gmx mdrun -s next.tpr -cpi state.cpt > > the following error appeared: > > > *Output file appending has been requested,* > *but some output files listed in the checkpoint file md_0_1.cpt* > *are not present or not named as the output files by the current program:* > *Expect output files present:* > > *Expected output files not present or named differently:* > * md_0_1.log* > * md_0_1.xtc* > * md_0_1.edr* > > *---* > *Program: gmx mdrun, version 2016.4* > *Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)* > > *Fatal error:* > *File appending requested, but 3 of the 3 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 you used -deffnm and the > files* > *listed above as not present are in fact present, try explicitly > specifying* > *them in respective mdrun options. 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 do not understand. the input files are correct. > > Em qui, 8 de nov de 2018 às 14:13, < > gromacs.org_gmx-users-requ...@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. start the simulation of the last stopping point. (Edjan Silva) > >2. Re: start the simulation of the last stopping point. (Paul Bauer) > >3. Re: DispErsion correction (Farial Tavakoli) > >4. Assigning charge to closely related functional group > > (Tushar Ranjan Moharana) > >5. 4. Re: 5. Re: 3. Re: Strange pullx coordinates (PMF > > (CROUZY Serge 119222) > > > > > > -- > > > > Message: 1 > > Date: Thu, 8 Nov 2018 10:23:13 -0300 > > From: Edjan Silva > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: [gmx-users] start the simulation of the last stopping point. > > Message-ID: > > < > > capf4pyb-pq8bbtfr3o5sfasl42jgwvu5kusle8l4l8sdi1y...@mail.gmail.com> > > Content-Type: text/plain; charset="UTF-8" > > > > Dear fellow scientists, > > > > I'm doing a 40ns simulation between DNA and a small molecule. It occurred > > that around 30 nanoseconds, the computer hung up. > > > > How do I start the simulation from the 30 nanoseconds performed? > > > > > > -- > > > > Message: 2 > > Date: Thu, 8 Nov 2018 14:22:56 +0100 > > From: Paul Bauer > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: Re: [gmx-users] start the simulation of the last stopping > > point. > > Message-ID: <6edfea12-973e-15e2-4d3d-86f67c1dc...@gmail.com> > > Content-Type: text/plain; charset=utf-8; format=flowed > > > > Hello, > > > > you can find information on how to extend simulations here: > > > > > http://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html > > > > Cheers > > > > Paul > > > > On 2018-11-08 14:23, Edjan Silva wrote: > > > Dear fellow scientists, > > > > > > I'm doing a 40ns simulation between DNA and a small molecule. It > occurred > > > that around 30 nanoseconds, the computer hung up. > > > > > > How do I start the simulation from the 30 nanoseconds performed? > > > > > > -- > > > > Message: 3 > > Date: Thu, 8 Nov 2018 19:28:01 +0330 > > From: Farial Tavakoli > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] DispErsion correction > > Message-ID: > > < > > cadmafqhwfx8dpb2e8b1xyb6yyvba93p0jh3eyfq6wn5sxcm...@mail.gmail.com> > > Content-Type: text/plain; charset="UTF-8" > > > > Dear Justin and Dallas > > > > Thank you for your replying >
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 28 - start the simulation of the last stopping point.
Dear Paul, Thank you for your help. However, when you run the command: $ gmx convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr $ gmx mdrun -s next.tpr -cpi state.cpt the following error appeared: *Output file appending has been requested,* *but some output files listed in the checkpoint file md_0_1.cpt* *are not present or not named as the output files by the current program:* *Expect output files present:* *Expected output files not present or named differently:* * md_0_1.log* * md_0_1.xtc* * md_0_1.edr* *---* *Program: gmx mdrun, version 2016.4* *Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)* *Fatal error:* *File appending requested, but 3 of the 3 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 you used -deffnm and the files* *listed above as not present are in fact present, try explicitly specifying* *them in respective mdrun options. 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 do not understand. the input files are correct. Em qui, 8 de nov de 2018 às 14:13, < gromacs.org_gmx-users-requ...@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. start the simulation of the last stopping point. (Edjan Silva) >2. Re: start the simulation of the last stopping point. (Paul Bauer) >3. Re: DispErsion correction (Farial Tavakoli) >4. Assigning charge to closely related functional group > (Tushar Ranjan Moharana) >5. 4. Re: 5. Re: 3. Re: Strange pullx coordinates (PMF > (CROUZY Serge 119222) > > > -- > > Message: 1 > Date: Thu, 8 Nov 2018 10:23:13 -0300 > From: Edjan Silva > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] start the simulation of the last stopping point. > Message-ID: > < > capf4pyb-pq8bbtfr3o5sfasl42jgwvu5kusle8l4l8sdi1y...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear fellow scientists, > > I'm doing a 40ns simulation between DNA and a small molecule. It occurred > that around 30 nanoseconds, the computer hung up. > > How do I start the simulation from the 30 nanoseconds performed? > > > -- > > Message: 2 > Date: Thu, 8 Nov 2018 14:22:56 +0100 > From: Paul Bauer > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] start the simulation of the last stopping > point. > Message-ID: <6edfea12-973e-15e2-4d3d-86f67c1dc...@gmail.com> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hello, > > you can find information on how to extend simulations here: > > http://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html > > Cheers > > Paul > > On 2018-11-08 14:23, Edjan Silva wrote: > > Dear fellow scientists, > > > > I'm doing a 40ns simulation between DNA and a small molecule. It occurred > > that around 30 nanoseconds, the computer hung up. > > > > How do I start the simulation from the 30 nanoseconds performed? > > > -- > > Message: 3 > Date: Thu, 8 Nov 2018 19:28:01 +0330 > From: Farial Tavakoli > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] DispErsion correction > Message-ID: > < > cadmafqhwfx8dpb2e8b1xyb6yyvba93p0jh3eyfq6wn5sxcm...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear Justin and Dallas > > Thank you for your replying > > I have another problem in minimizing and NVT run of my complex, including a > protein and a peptidic ligand which the ligand has 2 phosphotyrosine > residues. I generated a topology file of ligand using ff14sb in ambertools > 16 and then converted the .inpcrd and .prmtop files in .gro and .top files > using acpype python script. The protein topology was generated using > amber99sb ff in GROMACS. >
