Re: [gmx-users] restart nvt run
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Dear Justin
Thank you so so much for your reply
Best regardsFarial
Sent from Yahoo Mail for iPhone
On Sunday, February 4, 2018, 5:22 PM, Justin Lemkul wrote:
On 2/4/18 8:50 AM, farial tavakoli wrote:
> Dear Justin
>
> Thank you so much for replying
> I dont know exactly how I should use gmx trjcat command to
> concatenate 2 .trr files (nvt.trr and traj.part0002.trr)
> I issued this command to merge them:
>
> gmx trjcat -f nvt.trr -o fixed.trr -cat
>
> but faced to this result:
>
> gmx trjcat -f nvt.trr -o fixed.trr -cat
>
This accomplishes nothing; nvt.trr and fixed.trr will be identical. The
purpose of trjcat is to assemble multiple trajectory files (note in the
help information, the -f argument specifies that it takes multiple
files). You want:
gmx trjcat -f nvt.trr traj.part0002.trr -o fixed.trr
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==
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Re: [gmx-users] restart nvt run
On 2/4/18 8:50 AM, farial tavakoli wrote: Dear Justin Thank you so much for replying I dont know exactly how I should use gmx trjcat command to concatenate 2 .trr files (nvt.trr and traj.part0002.trr) I issued this command to merge them: gmx trjcat -f nvt.trr -o fixed.trr -cat but faced to this result: gmx trjcat -f nvt.trr -o fixed.trr -cat This accomplishes nothing; nvt.trr and fixed.trr will be identical. The purpose of trjcat is to assemble multiple trajectory files (note in the help information, the -f argument specifies that it takes multiple files). You want: gmx trjcat -f nvt.trr traj.part0002.trr -o fixed.trr -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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.
Re: [gmx-users] restart nvt run
On 2/4/18 5:26 AM, farial tavakoli wrote: Dear GMX users I ran nvt simulation on my complex using gromacs2016.4. But faced to this error:File input/output error: Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space? so I deleted some files to make free space and then issued this command to restart the simulationgmx mdrun -s nvt.tpr -cpi nvt.cpt but faced to this error: Output file appending has been requested, but some output files listed in the checkpoint file nvt.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: nvt.log nvt.trr nvt.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." For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I renamed my files in this way:nvt.log to md.lognvt.edr to ener.edrnvt.trr to traj.trrnvt.cpt to state.cptnvt.tpr to topol.tpr but faced to the "fatal error" again. is there any one can help me? I dont want to use -noappend flag. Don't rename the files; that is the exact opposite of what you want to do. The error message is quite clear. The .cpt file expects files with certain names to be present. If you've removed, moved, or renamed them, appending will fail. If this is preventing you from moving ahead, just use -noappend and concatenate relevant output later. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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.
