[gmx-users] Keep having to path gromacs when opening a new terminal
Hello Users, I've compiled GROMACS successfully on my machine, but the gmx_mpi command is not recognized until I enter the command source /usr/local/gromacs/bin/GMXRC everything works fine after, but is there a way I can avoid having to enter that command every time I begin a new session? any help is appreciated, thank you! -Israel -- 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] XVG Plotting by Grace
try "xmgrace 'filename.xvg'" instead From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mahmoud Mirzaei Sent: Tuesday, June 18, 2019 6:31:25 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] XVG Plotting by Grace Dear GMX Users, in Gromacs 18.1, May you please kindly help me with this command: When I am trying to plot xvg by grace, I only see such thing... nanolab@nanolab:~/gx01$ grace pressure.xvg grace:1> grace:2> grace:3> grace:4> grace:5> grace:6> grace:7> grace:8> grace:9> grace:10> Many thanks. +Mahmoud -- Gromacs Users mailing list * Please search the archive at https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=02%7C01%7Cisraele%40cpp.edu%7C61d978a6191745e8815b08d6f3f153b3%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636964615157281032sdata=nAryc7o7qconbpVPJ%2F4LErXlQEjvEYibiqVDnN3TxRE%3Dreserved=0 before posting! * Can't post? Read https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Listsdata=02%7C01%7Cisraele%40cpp.edu%7C61d978a6191745e8815b08d6f3f153b3%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636964615157281032sdata=DG4VFIJw8X4uvreKhF%2FCn2iE%2BaxkPF%2B%2BQT7FDdCY7lI%3Dreserved=0 * For (un)subscribe requests visit https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-usersdata=02%7C01%7Cisraele%40cpp.edu%7C61d978a6191745e8815b08d6f3f153b3%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636964615157281032sdata=o7PsKmPGRR%2BZiMGxPsC7nqeLObSUgmnDZ7y6iOgPOfg%3Dreserved=0 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.
Re: [gmx-users] Grompp not producing tpr files
Great! Thanks!!! -Israel From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Dallas Warren Sent: Monday, June 17, 2019 10:31:43 PM To: GROMACS users Subject: Re: [gmx-users] Grompp not producing tpr files Before you go any further you need to correct the topology. The complete molecule should only have an integer charge, and if it does have a charge then neutralise the system with counter ions. https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FErrors%23System_has_non-zero_total_chargedata=02%7C01%7Cisraele%40cpp.edu%7C2e9ffeb3f8ad43fb2e1008d6f3ae51a3%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636964327356046756sdata=HGXGwqEHbNRahSnmfaF8AswV11uD0%2B%2B9wp6tjm%2FQRLg%3Dreserved=0 On Tue, 18 Jun. 2019, 1:17 pm Israel Estrada, wrote: > Thanks again for the replies, > > > I'm currently using gromacs 2019.3, and I'm creating a simple system with > only a monomer in water. The monomer's topology was created using TPP, for > use with the OPLS force field. > > > After adding the new residue to the force field, I'm able to run > "pdb2gmx", "editconf", and "solvate" with no issues to create the system. > It's when I try to "grompp" that the segmentation fault occurs. > > > The only thing that stands out is the system's charge. After running > pdb2gmx, the system's overall charge is listed as -1.589 e. > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Paul > Bauer > Sent: Thursday, June 13, 2019 8:08:58 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Grompp not producing tpr files > > Hello, > > Yes, the last part indicates an error that should not happen. > > Which version did you use to run this? > > If it is a version before 2018, can you try the newer versions to see if > the error persists? > > Cheers > > Paul > > > > On Thu, 13 Jun 2019, 17:04 Israel Estrada, wrote: > > > Thanks for the replies! > > > > Mark, the process seemed to "finish" properly (my terminal did not close, > > and the command line was waiting for the next command as if it ran > > normally). I looked for the output file (ions.tpr) in the working > > directory, or any new files, but nothing was generated. > > > > Bratin, here is what my terminal displayed, > > "command line: > > gmx grompp -f ions.mdp -c box.gro -o ions.tpr -p topol.top > > > > Setting the LD random seed to 973096069 > > Segmentation fault (core dumped)" > > The last part seems to be the error, right? > > > > Thanks again!! > > -Israel > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Bratin > > Kumar Das <177cy500.bra...@nitk.edu.in> > > Sent: Wednesday, June 12, 2019 7:00:55 PM > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Grompp not producing tpr files > > > > Hi > >Give here the full error > > > > On Thu 13 Jun, 2019, 1:35 AM Mark Abraham, > > wrote: > > > > > Hi, > > > > > > Was grompp exiting normally, or crashing? Are you looking in the right > > > place, for a file of the right name? :-) > > > > > > Mark > > > > > > On Wed., 12 Jun. 2019, 18:42 Israel Estrada, wrote: > > > > > > > Hello users, > > > > > > > > > > > > I'm running into problems trying to grompp; I'm using the command > > > > > > > > > > > > gmx grompp -f ions.mdp -c etc_box.gro -o ions.tpr -p topol.top > > > > > > > > > > > > and the process shows no error messages, but output files are not > being > > > > generated. I'm running this on a small molecule, about 20 atoms, with > > the > > > > hopes that I can modify OPLS parameters as needed. I'm sure the > problem > > > is > > > > related to an error in the topology files, but I don't know how or > if I > > > can > > > > fix this. > > > > > > > > > > > > Any help would be greatly appreciated, thank you! > > > > > > > > -Israel > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > > > https://nam03.safelinks.protection.outlook.com/?url=http
Re: [gmx-users] Grompp not producing tpr files
Thanks again for the replies, I'm currently using gromacs 2019.3, and I'm creating a simple system with only a monomer in water. The monomer's topology was created using TPP, for use with the OPLS force field. After adding the new residue to the force field, I'm able to run "pdb2gmx", "editconf", and "solvate" with no issues to create the system. It's when I try to "grompp" that the segmentation fault occurs. The only thing that stands out is the system's charge. After running pdb2gmx, the system's overall charge is listed as -1.589 e. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Paul Bauer Sent: Thursday, June 13, 2019 8:08:58 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Grompp not producing tpr files Hello, Yes, the last part indicates an error that should not happen. Which version did you use to run this? If it is a version before 2018, can you try the newer versions to see if the error persists? Cheers Paul On Thu, 13 Jun 2019, 17:04 Israel Estrada, wrote: > Thanks for the replies! > > Mark, the process seemed to "finish" properly (my terminal did not close, > and the command line was waiting for the next command as if it ran > normally). I looked for the output file (ions.tpr) in the working > directory, or any new files, but nothing was generated. > > Bratin, here is what my terminal displayed, > "command line: > gmx grompp -f ions.mdp -c box.gro -o ions.tpr -p topol.top > > Setting the LD random seed to 973096069 > Segmentation fault (core dumped)" > The last part seems to be the error, right? > > Thanks again!! > -Israel > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Bratin > Kumar Das <177cy500.bra...@nitk.edu.in> > Sent: Wednesday, June 12, 2019 7:00:55 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Grompp not producing tpr files > > Hi >Give here the full error > > On Thu 13 Jun, 2019, 1:35 AM Mark Abraham, > wrote: > > > Hi, > > > > Was grompp exiting normally, or crashing? Are you looking in the right > > place, for a file of the right name? :-) > > > > Mark > > > > On Wed., 12 Jun. 2019, 18:42 Israel Estrada, wrote: > > > > > Hello users, > > > > > > > > > I'm running into problems trying to grompp; I'm using the command > > > > > > > > > gmx grompp -f ions.mdp -c etc_box.gro -o ions.tpr -p topol.top > > > > > > > > > and the process shows no error messages, but output files are not being > > > generated. I'm running this on a small molecule, about 20 atoms, with > the > > > hopes that I can modify OPLS parameters as needed. I'm sure the problem > > is > > > related to an error in the topology files, but I don't know how or if I > > can > > > fix this. > > > > > > > > > Any help would be greatly appreciated, thank you! > > > > > > -Israel > > > -- > > > 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. > > > -- > 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 > https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.groma
Re: [gmx-users] Grompp not producing tpr files
Thanks for the replies! Mark, the process seemed to "finish" properly (my terminal did not close, and the command line was waiting for the next command as if it ran normally). I looked for the output file (ions.tpr) in the working directory, or any new files, but nothing was generated. Bratin, here is what my terminal displayed, "command line: gmx grompp -f ions.mdp -c box.gro -o ions.tpr -p topol.top Setting the LD random seed to 973096069 Segmentation fault (core dumped)" The last part seems to be the error, right? Thanks again!! -Israel From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Bratin Kumar Das <177cy500.bra...@nitk.edu.in> Sent: Wednesday, June 12, 2019 7:00:55 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Grompp not producing tpr files Hi Give here the full error On Thu 13 Jun, 2019, 1:35 AM Mark Abraham, wrote: > Hi, > > Was grompp exiting normally, or crashing? Are you looking in the right > place, for a file of the right name? :-) > > Mark > > On Wed., 12 Jun. 2019, 18:42 Israel Estrada, wrote: > > > Hello users, > > > > > > I'm running into problems trying to grompp; I'm using the command > > > > > > gmx grompp -f ions.mdp -c etc_box.gro -o ions.tpr -p topol.top > > > > > > and the process shows no error messages, but output files are not being > > generated. I'm running this on a small molecule, about 20 atoms, with the > > hopes that I can modify OPLS parameters as needed. I'm sure the problem > is > > related to an error in the topology files, but I don't know how or if I > can > > fix this. > > > > > > Any help would be greatly appreciated, thank you! > > > > -Israel > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=02%7C01%7Cisraele%40cpp.edu%7Cffac6cb3efc64f49b25008d6efa30958%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636959880859561003sdata=srifcVMGyR34i8jY1w3JwmR%2F25Azq3Bf%2Ft39u5u82wc%3Dreserved=0 > > before > > posting! > > > > * Can't post? Read > > https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Listsdata=02%7C01%7Cisraele%40cpp.edu%7Cffac6cb3efc64f49b25008d6efa30958%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636959880859561003sdata=xoBSwamQTLamMjgsmqCbyeqUt17BQ2h%2BqcOYCfQKoI4%3Dreserved=0 > > > > * For (un)subscribe requests visit > > https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-usersdata=02%7C01%7Cisraele%40cpp.edu%7Cffac6cb3efc64f49b25008d6efa30958%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636959880859561003sdata=B9%2FLxGhb2H0ancau90hPfnPDt1Exu3RAAlInINB0X0w%3Dreserved=0 > > or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=02%7C01%7Cisraele%40cpp.edu%7Cffac6cb3efc64f49b25008d6efa30958%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636959880859561003sdata=srifcVMGyR34i8jY1w3JwmR%2F25Azq3Bf%2Ft39u5u82wc%3Dreserved=0 > before > posting! > > * Can't post? Read > https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Listsdata=02%7C01%7Cisraele%40cpp.edu%7Cffac6cb3efc64f49b25008d6efa30958%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636959880859561003sdata=xoBSwamQTLamMjgsmqCbyeqUt17BQ2h%2BqcOYCfQKoI4%3Dreserved=0 > > * For (un)subscribe requests visit > https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-usersdata=02%7C01%7Cisraele%40cpp.edu%7Cffac6cb3efc64f49b25008d6efa30958%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636959880859561003sdata=B9%2FLxGhb2H0ancau90hPfnPDt1Exu3RAAlInINB0X0w%3Dreserved=0 > or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=02%7C01%7Cisraele%40cpp.edu%7Cffac6cb3efc64f49b25008d6efa30958%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636959880859561003sdata=srifcVMGyR34i8jY1w3JwmR%2F25Azq3Bf%2Ft39u5u82wc%3Dreserved=0 before posting! * Can't post? Read https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Listsdata=02%7C01%7Cisraele%40cpp.edu%7Cffac6cb3efc64f49b25008d6efa30958%7C164ba61
[gmx-users] Grompp not producing tpr files
Hello users, I'm running into problems trying to grompp; I'm using the command gmx grompp -f ions.mdp -c etc_box.gro -o ions.tpr -p topol.top and the process shows no error messages, but output files are not being generated. I'm running this on a small molecule, about 20 atoms, with the hopes that I can modify OPLS parameters as needed. I'm sure the problem is related to an error in the topology files, but I don't know how or if I can fix this. Any help would be greatly appreciated, thank you! -Israel -- 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] Fw: Attempting REMD tutorial by Mark Abraham
From: Israel Estrada Sent: Wednesday, May 29, 2019 3:15 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Attempting REMD tutorial by Mark Abraham Hi all, I'm attempting to follow Mark Abraham's introduction to REMD. (http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B) I'm currently attempting and failing to run REMD equilibriations in stage 1, using the command: mpirun -np 4 mdrun_mpi -v -multidir equil[0123] However, I'm receiving an error "mpirun: cannot start mdrun_mpi on n0 (o): No such file or directory" Any guidance would be very much appreciated. I'm certain it's a fairly simple fix, I'm just not well versed in this yet. Thank you! -Israel -- 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.
