Re: [gmx-users] QUERY IN GRO FILE
Hi, Yeah, both confout.gro and em.gro are same for the same tpr input file. The -deffnm flag is to indicate the names you want to give to your output files. Incase the -deffnm flag is missing GROMACS gives default names. Regards, Amit Behera REsearch Scholar, IISc, Bangalore. > -- > > Message: 3 > Date: Thu, 30 Mar 2017 11:23:03 +0530 > From: Neha Gupta <nehaphysic...@gmail.com> > To: gmx-us...@gromacs.org > Subject: [gmx-users] QUERY IN GRO FILE > Message-ID: > <canoqod4kpuznconja-jxmzkjqv7bv82qrxbmkm1izmc7rvd...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi gromacs users, > > > I have a doubt in this command, > > grompp -f em.mdp -c conf.gro -p topol.top -o em the output file from grompp command should be tpr. so it should be " -o em.tpr" because mdrun will take that tpr file as input. > mdrun -v -deffnm em > > > These commands generate em.gro, em.tpr, em.trr, em.log file. > > > There is another command which is > > > mdrun -s em.tpr > > which generates confout.gro > > Does em.gro and confout.gro are one and the same? > > What are the technical differences? > > > Thanks, > > Neha -- 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] QUERY IN GRO FILE
Those are not two different commands, rather the same command with different options. If you are not familiar with the options of the command, then mdrun -h will list them for you. Specifically, in the second instance of mdrun you get the default output file name confout.gro whereas in the first instance you have changed all the output files to be em.sometype. Peter -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Neha Gupta Sent: Thursday, March 30, 2017 8:53 AM To: gmx-us...@gromacs.org Subject: [gmx-users] QUERY IN GRO FILE Hi gromacs users, I have a doubt in this command, grompp -f em.mdp -c conf.gro -p topol.top -o em mdrun -v -deffnm em These commands generate em.gro, em.tpr, em.trr, em.log file. There is another command which is mdrun -s em.tpr which generates confout.gro Does em.gro and confout.gro are one and the same? What are the technical differences? Thanks, Neha -- 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.
[gmx-users] QUERY IN GRO FILE
Hi gromacs users, I have a doubt in this command, grompp -f em.mdp -c conf.gro -p topol.top -o em mdrun -v -deffnm em These commands generate em.gro, em.tpr, em.trr, em.log file. There is another command which is mdrun -s em.tpr which generates confout.gro Does em.gro and confout.gro are one and the same? What are the technical differences? Thanks, Neha -- 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.
