Re: [gmx-users] Number of coordinates in .gro file does not match topology
Hi, Check your box size,I had a same problem. I used a larger box then the problem solved. Best Ali On Mon, Oct 30, 2017 at 6:29 PM, Mark Abraham wrote: > Hi, > > How big is the system before and after? Gro format used fixed columns, so > can sometimes struggle with large systems. Try using .g96 as the output > file extension > > Mark > > On Mon, 30 Oct 2017 17:29 wrote: > > > Checked the file again. It is the one that gets generated after the > > solvation command is run. > > > > Sent from my iPhone > > > > > On 30-Oct-2017, at 9:39 PM, Mark Abraham > > wrote: > > > > > > Hi, > > > > > > The most likely scenario is that you are looking at a gro file that is > > not > > > the one that was written by the solvation tool. > > > > > > Mark > > > > > > On Mon, Oct 30, 2017 at 9:41 AM Aishwarya Smriti < > > > smritiaishwary...@gmail.com> wrote: > > > > > >> Hi! > > >> > > >> I'm trying to solvate a system of a CNT and a protein molecule. My > > updated > > >> topology file shows 106275 new solvent molecules added but the .gro > file > > >> has only coordinates for 6197 new molecules. I'm using SPC model for > > >> solvating, Please help. > > >> > > >> Regards, > > >> Aishwarya Smriti > > >> Senior Undergraduate > > >> Chemical Engineering > > >> Indian Institute of Technology, Delhi > > >> -- > > >> 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 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.
Re: [gmx-users] Number of coordinates in .gro file does not match topology
Hi, How big is the system before and after? Gro format used fixed columns, so can sometimes struggle with large systems. Try using .g96 as the output file extension Mark On Mon, 30 Oct 2017 17:29 wrote: > Checked the file again. It is the one that gets generated after the > solvation command is run. > > Sent from my iPhone > > > On 30-Oct-2017, at 9:39 PM, Mark Abraham > wrote: > > > > Hi, > > > > The most likely scenario is that you are looking at a gro file that is > not > > the one that was written by the solvation tool. > > > > Mark > > > > On Mon, Oct 30, 2017 at 9:41 AM Aishwarya Smriti < > > smritiaishwary...@gmail.com> wrote: > > > >> Hi! > >> > >> I'm trying to solvate a system of a CNT and a protein molecule. My > updated > >> topology file shows 106275 new solvent molecules added but the .gro file > >> has only coordinates for 6197 new molecules. I'm using SPC model for > >> solvating, Please help. > >> > >> Regards, > >> Aishwarya Smriti > >> Senior Undergraduate > >> Chemical Engineering > >> Indian Institute of Technology, Delhi > >> -- > >> 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 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] Number of coordinates in .gro file does not match topology
Checked the file again. It is the one that gets generated after the solvation command is run. Sent from my iPhone > On 30-Oct-2017, at 9:39 PM, Mark Abraham wrote: > > Hi, > > The most likely scenario is that you are looking at a gro file that is not > the one that was written by the solvation tool. > > Mark > > On Mon, Oct 30, 2017 at 9:41 AM Aishwarya Smriti < > smritiaishwary...@gmail.com> wrote: > >> Hi! >> >> I'm trying to solvate a system of a CNT and a protein molecule. My updated >> topology file shows 106275 new solvent molecules added but the .gro file >> has only coordinates for 6197 new molecules. I'm using SPC model for >> solvating, Please help. >> >> Regards, >> Aishwarya Smriti >> Senior Undergraduate >> Chemical Engineering >> Indian Institute of Technology, Delhi >> -- >> 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.
Re: [gmx-users] Number of coordinates in .gro file does not match topology
Hi, The most likely scenario is that you are looking at a gro file that is not the one that was written by the solvation tool. Mark On Mon, Oct 30, 2017 at 9:41 AM Aishwarya Smriti < smritiaishwary...@gmail.com> wrote: > Hi! > > I'm trying to solvate a system of a CNT and a protein molecule. My updated > topology file shows 106275 new solvent molecules added but the .gro file > has only coordinates for 6197 new molecules. I'm using SPC model for > solvating, Please help. > > Regards, > Aishwarya Smriti > Senior Undergraduate > Chemical Engineering > Indian Institute of Technology, Delhi > -- > 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.
Re: [gmx-users] Number of coordinates in .gro file does not match topology
You do something wrong. How you solvate?Try something like this: gmx solvate -cp my_system.gro -cs spc216.gro -o my_system_solv.gro -p topol.top On Monday, October 30, 2017, 10:41:31 AM GMT+2, Aishwarya Smriti wrote: Hi! I'm trying to solvate a system of a CNT and a protein molecule. My updated topology file shows 106275 new solvent molecules added but the .gro file has only coordinates for 6197 new molecules. I'm using SPC model for solvating, Please help. Regards, Aishwarya Smriti Senior Undergraduate Chemical Engineering Indian Institute of Technology, Delhi -- 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] Number of coordinates in .gro file does not match topology
Hi! I'm trying to solvate a system of a CNT and a protein molecule. My updated topology file shows 106275 new solvent molecules added but the .gro file has only coordinates for 6197 new molecules. I'm using SPC model for solvating, Please help. Regards, Aishwarya Smriti Senior Undergraduate Chemical Engineering Indian Institute of Technology, Delhi -- 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.