Thanks Dr. Dallas for your replying. But my friend told me that the extended one is only 2 ns not the total 22ns.
So,the gro for the extended one is not affect at all? I thought that the gro file that prodice from the extend one is only 2 ns. Thanks Doc! On Wed, Mar 13, 2013 at 11:19 AM, Dallas Warren [via GROMACS] <ml-node+s5086n5006280...@n6.nabble.com> wrote: > Why is it that you want to combine the two coordinate files? > > md.gro is the coordinates of the system at the end of 20ns. > > md_extend.gro is the coordinates of the system at the end of 22ns. > > So combining them will not make much sense. > > Catch ya, > > Dr. Dallas Warren > Drug Discovery Biology > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > [hidden email] > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > >> -----Original Message----- >> From: [hidden email] [mailto:gmx-users- >> [hidden email]] On Behalf Of Nur Syafiqah Abdul Ghani >> Sent: Wednesday, 13 March 2013 2:10 PM >> To: [hidden email] >> Subject: [gmx-users] combine two gro files >> >> Hi all, >> >> I just finished my simulation protein in mix solvent with the file >> name md.gro but when i analyze the protein it seems not stable yet >> therefore i have to extend it about 2ns more.The previously i used >> 20ns for my simulation.So the extended oneis name md_extend.gro and >> also the others file, trr tpr. >> >> The command that i used to extend the simu is like below : >> tpbconv -f md.trr -s md.tpr -o md_extend.tpr -extend 2000 >> mdrun -v -cpi md.cpt -deffnm md_extend >> >> >From what I understand the new file that created after extend is only >> 2ns second.right? >> How i can combine the gro file from the original and the extended one? >> Because the xtc trr and also edr file i combine it by using comand >> trjcat and eneconv. >> >> The trjcat cant combine the gro file because the error stated : >> Fatal error: >> Can not write a gro file without atom names >> >> So anyone facing this problems.?I already search in previous problem >> but they said convert the gro to pdb?then use command cat..can i use >> that? >> >> -- >> Best Regards, >> >> Nur Syafiqah Abdul Ghani, >> Theoretical and Computational Chemistry Laboratory, >> Department of Chemistry, >> Faculty of Science, >> Universiti Putra Malaysia, >> 43400 Serdang, >> Selangor. >> alternative email : [hidden email] >> -- >> gmx-users mailing list [hidden email] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [hidden email]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [hidden email] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [hidden email]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > ________________________________ > If you reply to this email, your message will be added to the discussion > below: > http://gromacs.5086.n6.nabble.com/combine-two-gro-files-tp5006279p5006280.html > To start a new topic under GROMACS Users Forum, email > ml-node+s5086n4370410...@n6.nabble.com > To unsubscribe from GROMACS, click here. > NAML -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : syafiqahabdulgh...@gmail.com -- View this message in context: http://gromacs.5086.n6.nabble.com/combine-two-gro-files-tp5006279p5006281.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
