Re: [gmx-users] trjconv (File input/output error)
Den 2018-08-13 kl. 20:56, skrev Andrew Bostick: Dear gromacs users For fixing PBC problem, I used following command: gmx_mpi trjconv -f md.trr -s md.tpr -n index.ndx -o new.xtc -pbc nojump But I encountered with: Program gmx trjconv, VERSION 5.1.3 Source code file: /root/gromacs_source/gromacs-5.1.3/src/gromacs/utility/futil.cpp, line: 469 File input/output error: new.xtc For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors. How to solve that? Full disk? No permission? -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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] trjconv ndec not working
On 4/18/18 8:57 AM, Dawid das wrote: The quick and dirty solution is that I write gro and g96 and copy coordinates from the latter to the former, but I'd rather have more elaborate solution. .gro files are fixed-format, and in current GROMACS versions it is not possible to write more decimal places than the file format specification allows. GROMACS can read .gro files with variable precision for backwards-compatibility, but for consistency (especially with external programs that also read .gro), it is not possible to get variable precision output to .gro from any GROMACS program. If you need greater precision, just use .g96 directly rather than copying back to a .gro file. -Justin 2018-04-18 14:53 GMT+02:00 Dawid das : Dear All, I have similar issue. I have created xtc file with precision of 1.0e-6 nm and I want my gro file to have the same precision, and I get this at the end of trjconv Reading frame 0 time3.000 Precision of npt-md-prod.xtc is 1e-06 (nm) Setting output precision to 1e-06 (nm) Last frame 0 time3.000 So isn't there really a way to overcome that? For instance recompile Gromacs? Best wishes, Dawid Grabarek 2018-04-17 18:48 GMT+02:00 Eric Smoll : Paul and Mark, Thanks for the reply! Good to know I wasn't doing anything wrong. Best, Eric On Tue, Apr 17, 2018 at 10:08 AM, Mark Abraham wrote: Hi, What Paul said agrees with my memory, but I'd not found time to check that yet. We should indeed fix the docs. Mark On Tue, Apr 17, 2018, 16:42 Paul Bauer wrote: Hello Eric, I had a look at the code for writing gro files and it looks to me that it is only able to write three decimal places there. There is a comment in the code that mentions that writing other precisions has been removed. This means that we need to update the man page text to not be confusing. Cheers Paul On 2018-04-15 17:45, Eric Smoll wrote: Hello Joe, Thanks for the reply. Sorry if I was not clear. I provide a gro file with high precision (7 decimal places). For some reason, the output gro always has three decimal places. The manual for trjconv suggests that the output should have 7 decimal places. Best, Eric On Apr 15, 2018, at 4:00 AM, Joe Jordan wrote: Are you trying to write from an xtc file? If so, does it have the necessary precision? On Sun, Apr 15, 2018 at 4:53 AM, Eric Smoll wrote: Hello Gromacs Users, I am using Gromacs 2018.1. The manual page for gmx trjconv states the number of decimal places in the output of a gro file is taken from the number of decimal places in the input unless the ndec flag is set. The ndec flag can be used to increase precision in the output. However, providing trjconv a gro file with increased coordinate precision (7 decimal places) does not increase the precision of the output gro file. Also, the ndec flag has no impact on the output precision. My input gro is written as follows: comment 10 1ABC C11 -0.1204914 -0.0759159 -0.0131147 ...etc. trconv does not complain about this file format and creates a normal, three decimal gro file as output. Has this feature been removed? Best, Eric -- 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. -- Joe Jordan -- 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] trjconv ndec not working
The quick and dirty solution is that I write gro and g96 and copy coordinates from the latter to the former, but I'd rather have more elaborate solution. 2018-04-18 14:53 GMT+02:00 Dawid das : > Dear All, > > I have similar issue. I have created xtc file with precision of 1.0e-6 nm > and I want my gro file to have the same precision, > and I get this at the end of trjconv > > Reading frame 0 time3.000 > Precision of npt-md-prod.xtc is 1e-06 (nm) > > Setting output precision to 1e-06 (nm) > Last frame 0 time3.000 > > So isn't there really a way to overcome that? For instance recompile > Gromacs? > > Best wishes, > Dawid Grabarek > > 2018-04-17 18:48 GMT+02:00 Eric Smoll : > >> Paul and Mark, >> >> Thanks for the reply! Good to know I wasn't doing anything wrong. >> >> Best, >> Eric >> >> On Tue, Apr 17, 2018 at 10:08 AM, Mark Abraham >> wrote: >> >> > Hi, >> > >> > What Paul said agrees with my memory, but I'd not found time to check >> that >> > yet. We should indeed fix the docs. >> > >> > Mark >> > >> > On Tue, Apr 17, 2018, 16:42 Paul Bauer wrote: >> > >> > > Hello Eric, >> > > >> > > I had a look at the code for writing gro files and it looks to me that >> > > it is only able to write three decimal places there. >> > > There is a comment in the code that mentions that writing other >> > > precisions has been removed. >> > > This means that we need to update the man page text to not be >> confusing. >> > > >> > > Cheers >> > > >> > > Paul >> > > >> > > >> > > On 2018-04-15 17:45, Eric Smoll wrote: >> > > > Hello Joe, >> > > > >> > > > Thanks for the reply. Sorry if I was not clear. I provide a gro file >> > > with high precision (7 decimal places). For some reason, the output >> gro >> > > always has three decimal places. The manual for trjconv suggests >> that >> > the >> > > output should have 7 decimal places. >> > > > >> > > > Best, >> > > > Eric >> > > > >> > > >> On Apr 15, 2018, at 4:00 AM, Joe Jordan >> > wrote: >> > > >> >> > > >> Are you trying to write from an xtc file? If so, does it have the >> > > necessary >> > > >> precision? >> > > >> >> > > >>> On Sun, Apr 15, 2018 at 4:53 AM, Eric Smoll >> > > wrote: >> > > >>> >> > > >>> Hello Gromacs Users, >> > > >>> >> > > >>> I am using Gromacs 2018.1. >> > > >>> >> > > >>> The manual page for gmx trjconv states the number of decimal >> places >> > in >> > > the >> > > >>> output of a gro file is taken from the number of decimal places in >> > the >> > > >>> input unless the ndec flag is set. The ndec flag can be used to >> > > increase >> > > >>> precision in the output. >> > > >>> >> > > >>> However, providing trjconv a gro file with increased coordinate >> > > precision >> > > >>> (7 decimal places) does not increase the precision of the output >> gro >> > > file. >> > > >>> Also, the ndec flag has no impact on the output precision. >> > > >>> >> > > >>> My input gro is written as follows: >> > > >>> >> > > >>> comment >> > > >>> 10 >> > > >>> 1ABC C11 -0.1204914 -0.0759159 -0.0131147 >> > > >>> ...etc. >> > > >>> >> > > >>> trconv does not complain about this file format and creates a >> normal, >> > > three >> > > >>> decimal >> > > >>> gro file as output. >> > > >>> >> > > >>> Has this feature been removed? >> > > >>> >> > > >>> Best, >> > > >>> Eric >> > > >>> -- >> > > >>> 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. >> > > >>> >> > > >> >> > > >> >> > > >> -- >> > > >> Joe Jordan >> > > >> -- >> > > >> 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.or
Re: [gmx-users] trjconv ndec not working
Dear All, I have similar issue. I have created xtc file with precision of 1.0e-6 nm and I want my gro file to have the same precision, and I get this at the end of trjconv Reading frame 0 time3.000 Precision of npt-md-prod.xtc is 1e-06 (nm) Setting output precision to 1e-06 (nm) Last frame 0 time3.000 So isn't there really a way to overcome that? For instance recompile Gromacs? Best wishes, Dawid Grabarek 2018-04-17 18:48 GMT+02:00 Eric Smoll : > Paul and Mark, > > Thanks for the reply! Good to know I wasn't doing anything wrong. > > Best, > Eric > > On Tue, Apr 17, 2018 at 10:08 AM, Mark Abraham > wrote: > > > Hi, > > > > What Paul said agrees with my memory, but I'd not found time to check > that > > yet. We should indeed fix the docs. > > > > Mark > > > > On Tue, Apr 17, 2018, 16:42 Paul Bauer wrote: > > > > > Hello Eric, > > > > > > I had a look at the code for writing gro files and it looks to me that > > > it is only able to write three decimal places there. > > > There is a comment in the code that mentions that writing other > > > precisions has been removed. > > > This means that we need to update the man page text to not be > confusing. > > > > > > Cheers > > > > > > Paul > > > > > > > > > On 2018-04-15 17:45, Eric Smoll wrote: > > > > Hello Joe, > > > > > > > > Thanks for the reply. Sorry if I was not clear. I provide a gro file > > > with high precision (7 decimal places). For some reason, the output gro > > > always has three decimal places. The manual for trjconv suggests that > > the > > > output should have 7 decimal places. > > > > > > > > Best, > > > > Eric > > > > > > > >> On Apr 15, 2018, at 4:00 AM, Joe Jordan > > wrote: > > > >> > > > >> Are you trying to write from an xtc file? If so, does it have the > > > necessary > > > >> precision? > > > >> > > > >>> On Sun, Apr 15, 2018 at 4:53 AM, Eric Smoll > > > wrote: > > > >>> > > > >>> Hello Gromacs Users, > > > >>> > > > >>> I am using Gromacs 2018.1. > > > >>> > > > >>> The manual page for gmx trjconv states the number of decimal places > > in > > > the > > > >>> output of a gro file is taken from the number of decimal places in > > the > > > >>> input unless the ndec flag is set. The ndec flag can be used to > > > increase > > > >>> precision in the output. > > > >>> > > > >>> However, providing trjconv a gro file with increased coordinate > > > precision > > > >>> (7 decimal places) does not increase the precision of the output > gro > > > file. > > > >>> Also, the ndec flag has no impact on the output precision. > > > >>> > > > >>> My input gro is written as follows: > > > >>> > > > >>> comment > > > >>> 10 > > > >>> 1ABC C11 -0.1204914 -0.0759159 -0.0131147 > > > >>> ...etc. > > > >>> > > > >>> trconv does not complain about this file format and creates a > normal, > > > three > > > >>> decimal > > > >>> gro file as output. > > > >>> > > > >>> Has this feature been removed? > > > >>> > > > >>> Best, > > > >>> Eric > > > >>> -- > > > >>> 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. > > > >>> > > > >> > > > >> > > > >> -- > > > >> Joe Jordan > > > >> -- > > > >> 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.
Re: [gmx-users] trjconv ndec not working
Paul and Mark, Thanks for the reply! Good to know I wasn't doing anything wrong. Best, Eric On Tue, Apr 17, 2018 at 10:08 AM, Mark Abraham wrote: > Hi, > > What Paul said agrees with my memory, but I'd not found time to check that > yet. We should indeed fix the docs. > > Mark > > On Tue, Apr 17, 2018, 16:42 Paul Bauer wrote: > > > Hello Eric, > > > > I had a look at the code for writing gro files and it looks to me that > > it is only able to write three decimal places there. > > There is a comment in the code that mentions that writing other > > precisions has been removed. > > This means that we need to update the man page text to not be confusing. > > > > Cheers > > > > Paul > > > > > > On 2018-04-15 17:45, Eric Smoll wrote: > > > Hello Joe, > > > > > > Thanks for the reply. Sorry if I was not clear. I provide a gro file > > with high precision (7 decimal places). For some reason, the output gro > > always has three decimal places. The manual for trjconv suggests that > the > > output should have 7 decimal places. > > > > > > Best, > > > Eric > > > > > >> On Apr 15, 2018, at 4:00 AM, Joe Jordan > wrote: > > >> > > >> Are you trying to write from an xtc file? If so, does it have the > > necessary > > >> precision? > > >> > > >>> On Sun, Apr 15, 2018 at 4:53 AM, Eric Smoll > > wrote: > > >>> > > >>> Hello Gromacs Users, > > >>> > > >>> I am using Gromacs 2018.1. > > >>> > > >>> The manual page for gmx trjconv states the number of decimal places > in > > the > > >>> output of a gro file is taken from the number of decimal places in > the > > >>> input unless the ndec flag is set. The ndec flag can be used to > > increase > > >>> precision in the output. > > >>> > > >>> However, providing trjconv a gro file with increased coordinate > > precision > > >>> (7 decimal places) does not increase the precision of the output gro > > file. > > >>> Also, the ndec flag has no impact on the output precision. > > >>> > > >>> My input gro is written as follows: > > >>> > > >>> comment > > >>> 10 > > >>> 1ABC C11 -0.1204914 -0.0759159 -0.0131147 > > >>> ...etc. > > >>> > > >>> trconv does not complain about this file format and creates a normal, > > three > > >>> decimal > > >>> gro file as output. > > >>> > > >>> Has this feature been removed? > > >>> > > >>> Best, > > >>> Eric > > >>> -- > > >>> 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. > > >>> > > >> > > >> > > >> -- > > >> Joe Jordan > > >> -- > > >> 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] trjconv ndec not working
Hi, What Paul said agrees with my memory, but I'd not found time to check that yet. We should indeed fix the docs. Mark On Tue, Apr 17, 2018, 16:42 Paul Bauer wrote: > Hello Eric, > > I had a look at the code for writing gro files and it looks to me that > it is only able to write three decimal places there. > There is a comment in the code that mentions that writing other > precisions has been removed. > This means that we need to update the man page text to not be confusing. > > Cheers > > Paul > > > On 2018-04-15 17:45, Eric Smoll wrote: > > Hello Joe, > > > > Thanks for the reply. Sorry if I was not clear. I provide a gro file > with high precision (7 decimal places). For some reason, the output gro > always has three decimal places. The manual for trjconv suggests that the > output should have 7 decimal places. > > > > Best, > > Eric > > > >> On Apr 15, 2018, at 4:00 AM, Joe Jordan wrote: > >> > >> Are you trying to write from an xtc file? If so, does it have the > necessary > >> precision? > >> > >>> On Sun, Apr 15, 2018 at 4:53 AM, Eric Smoll > wrote: > >>> > >>> Hello Gromacs Users, > >>> > >>> I am using Gromacs 2018.1. > >>> > >>> The manual page for gmx trjconv states the number of decimal places in > the > >>> output of a gro file is taken from the number of decimal places in the > >>> input unless the ndec flag is set. The ndec flag can be used to > increase > >>> precision in the output. > >>> > >>> However, providing trjconv a gro file with increased coordinate > precision > >>> (7 decimal places) does not increase the precision of the output gro > file. > >>> Also, the ndec flag has no impact on the output precision. > >>> > >>> My input gro is written as follows: > >>> > >>> comment > >>> 10 > >>> 1ABC C11 -0.1204914 -0.0759159 -0.0131147 > >>> ...etc. > >>> > >>> trconv does not complain about this file format and creates a normal, > three > >>> decimal > >>> gro file as output. > >>> > >>> Has this feature been removed? > >>> > >>> Best, > >>> Eric > >>> -- > >>> 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. > >>> > >> > >> > >> -- > >> Joe Jordan > >> -- > >> 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] trjconv ndec not working
Hello Eric, I had a look at the code for writing gro files and it looks to me that it is only able to write three decimal places there. There is a comment in the code that mentions that writing other precisions has been removed. This means that we need to update the man page text to not be confusing. Cheers Paul On 2018-04-15 17:45, Eric Smoll wrote: Hello Joe, Thanks for the reply. Sorry if I was not clear. I provide a gro file with high precision (7 decimal places). For some reason, the output gro always has three decimal places. The manual for trjconv suggests that the output should have 7 decimal places. Best, Eric On Apr 15, 2018, at 4:00 AM, Joe Jordan wrote: Are you trying to write from an xtc file? If so, does it have the necessary precision? On Sun, Apr 15, 2018 at 4:53 AM, Eric Smoll wrote: Hello Gromacs Users, I am using Gromacs 2018.1. The manual page for gmx trjconv states the number of decimal places in the output of a gro file is taken from the number of decimal places in the input unless the ndec flag is set. The ndec flag can be used to increase precision in the output. However, providing trjconv a gro file with increased coordinate precision (7 decimal places) does not increase the precision of the output gro file. Also, the ndec flag has no impact on the output precision. My input gro is written as follows: comment 10 1ABC C11 -0.1204914 -0.0759159 -0.0131147 ...etc. trconv does not complain about this file format and creates a normal, three decimal gro file as output. Has this feature been removed? Best, Eric -- 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. -- Joe Jordan -- 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] trjconv ndec not working
Hello Joe, Thanks for the reply. Sorry if I was not clear. I provide a gro file with high precision (7 decimal places). For some reason, the output gro always has three decimal places. The manual for trjconv suggests that the output should have 7 decimal places. Best, Eric > On Apr 15, 2018, at 4:00 AM, Joe Jordan wrote: > > Are you trying to write from an xtc file? If so, does it have the necessary > precision? > >> On Sun, Apr 15, 2018 at 4:53 AM, Eric Smoll wrote: >> >> Hello Gromacs Users, >> >> I am using Gromacs 2018.1. >> >> The manual page for gmx trjconv states the number of decimal places in the >> output of a gro file is taken from the number of decimal places in the >> input unless the ndec flag is set. The ndec flag can be used to increase >> precision in the output. >> >> However, providing trjconv a gro file with increased coordinate precision >> (7 decimal places) does not increase the precision of the output gro file. >> Also, the ndec flag has no impact on the output precision. >> >> My input gro is written as follows: >> >> comment >> 10 >>1ABC C11 -0.1204914 -0.0759159 -0.0131147 >> ...etc. >> >> trconv does not complain about this file format and creates a normal, three >> decimal >> gro file as output. >> >> Has this feature been removed? >> >> Best, >> Eric >> -- >> 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. >> > > > > -- > Joe Jordan > -- > 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] trjconv ndec not working
Are you trying to write from an xtc file? If so, does it have the necessary precision? On Sun, Apr 15, 2018 at 4:53 AM, Eric Smoll wrote: > Hello Gromacs Users, > > I am using Gromacs 2018.1. > > The manual page for gmx trjconv states the number of decimal places in the > output of a gro file is taken from the number of decimal places in the > input unless the ndec flag is set. The ndec flag can be used to increase > precision in the output. > > However, providing trjconv a gro file with increased coordinate precision > (7 decimal places) does not increase the precision of the output gro file. > Also, the ndec flag has no impact on the output precision. > > My input gro is written as follows: > > comment > 10 > 1ABC C11 -0.1204914 -0.0759159 -0.0131147 > ...etc. > > trconv does not complain about this file format and creates a normal, three > decimal > gro file as output. > > Has this feature been removed? > > Best, > Eric > -- > 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. > -- Joe Jordan -- 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] trjconv -fit progressive
thanks Justin for your quick responce have a nice weekend Emiliano On 2017-09-08 17:59, Justin Lemkul wrote: On 9/8/17 11:57 AM, edesantis wrote: Hi gromacs users, I removed the boundary effects on my system box during the trajectory of protein crystal simulation following the Suggested trjconv workflow http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions then I need to fit the trj to remove rotations and translations (my propose is to reproduce a scattering pattern of the crystal, so I want that all frames are superimposable) so I tough to use -fit rot+trans looking at the trjconv manual I've seen also the flag -fit progressive, but actually I didn't understand what does this operation do, do you know it? It's described in the help info: "There are two options for fitting the trajectory to a reference either for essential dynamics analysis, etc. The first option is just plain fitting to a reference structure in the structure file. The second option is a progressive fit in which the first timeframe is fitted to the reference structure in the structure file to obtain and each subsequent timeframe is fitted to the previously fitted structure. This way a continuous trajectory is generated, which might not be the case when using the regular fit method, e.g. when your protein undergoes large conformational transitions." -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 == -- Emiliano De Santis -- 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] trjconv -fit progressive
On 9/8/17 11:57 AM, edesantis wrote: Hi gromacs users, I removed the boundary effects on my system box during the trajectory of protein crystal simulation following the Suggested trjconv workflow http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions then I need to fit the trj to remove rotations and translations (my propose is to reproduce a scattering pattern of the crystal, so I want that all frames are superimposable) so I tough to use -fit rot+trans looking at the trjconv manual I've seen also the flag -fit progressive, but actually I didn't understand what does this operation do, do you know it? It's described in the help info: "There are two options for fitting the trajectory to a reference either for essential dynamics analysis, etc. The first option is just plain fitting to a reference structure in the structure file. The second option is a progressive fit in which the first timeframe is fitted to the reference structure in the structure file to obtain and each subsequent timeframe is fitted to the previously fitted structure. This way a continuous trajectory is generated, which might not be the case when using the regular fit method, e.g. when your protein undergoes large conformational transitions." -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] trjconv not able to generated output
Sorry, my mistake. You better put me away with Zuckerberg and those guys. Have a good weekend! Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" To: "gmx-users" Sent: Friday, September 8, 2017 4:16:57 PM Subject: Re: [gmx-users] trjconv not able to generated output On 9/8/17 9:47 AM, Sergio Manzetti wrote: > I have done this many times before, its doesn't give any problems, it gives > the last frame and only that. But not in this case What do you mean? The screen output says it wrote a coordinate file at t=2000 ps. -Justin > > Sergio Manzetti > > [ http://www.fjordforsk.no/logo_hr2.jpg ] > > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] > Midtun > 6894 Vangsnes > Norge > Org.nr. 911 659 654 > Tlf: +47 57695621 > [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | > Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | > FAP ] > > > > From: "Justin Lemkul" > To: "gmx-users" > Sent: Friday, September 8, 2017 3:52:52 PM > Subject: Re: [gmx-users] trjconv not able to generated output > > On 9/8/17 9:38 AM, Sergio Manzetti wrote: >> Hi, I have tried several ways to get the last frame from the output xtc >> using gmx trjconv, like: >> >> sem@Fjordforsk:/media/sem/HDD3/files/sims/BPRP/5$ gmx trjconv -f traj_c -o >> confout.gro -b 2000 -e 2000 >> :-) GROMACS - gmx trjconv, VERSION 5.1.2 (-: >> >> GROMACS is written by: >> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar >> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch >> Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen >> Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner >> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff >> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk >> Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers >> Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf >> and the project leaders: >> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel >> >> Copyright (c) 1991-2000, University of Groningen, The Netherlands. >> Copyright (c) 2001-2015, The GROMACS development team at >> Uppsala University, Stockholm University and >> the Royal Institute of Technology, Sweden. >> check out http://www.gromacs.org for more information. >> >> GROMACS is free software; you can redistribute it and/or modify it >> under the terms of the GNU Lesser General Public License >> as published by the Free Software Foundation; either version 2.1 >> of the License, or (at your option) any later version. >> >> GROMACS: gmx trjconv, VERSION 5.1.2 >> Executable: /usr/bin/gmx >> Data prefix: /usr >> Command line: >> gmx trjconv -f traj_c -o confout.gro -b 2000 -e 2000 >> >> Will write gro: Coordinate file in Gromos-87 format >> Reading file topol.tpr, VERSION 5.1.2 (single precision) >> Reading file topol.tpr, VERSION 5.1.2 (single precision) >> Select group for output >> Group 0 ( System) has 50510 elements >> Group 1 ( DNA) has 1333 elements >> Group 2 ( NA) has 71 elements >> Group 3 ( CL) has 31 elements >> Group 4 ( PRB) has 28 elements >> Group 5 ( Ion) has 102 elements >> Group 6 ( NA) has 71 elements >> Group 7 ( CL) has 31 elements >> Group 8 ( PRB) has 28 elements >> Group 9 ( Other) has 28 elements >> Group 10 ( NA) has 71 elements >> Group 11 ( CL) has 31 elements >> Group 12 ( PRB) has 28 elements >> Group 13 ( Water) has 49047 elements >> Group 14 ( SOL) has 49047 elements >> Group 15 ( non-Water) has 1463 elements >> Group 16 ( Water_and_ions) has 49149 elements >> Select a group: 15 >> Selected 15: 'non-Water' >> Reading frame 0 time 2000.000 >> Precision of traj_c.xtc is 0.001 (nm) >> Using output precision of 0.001 (nm) >> >> Back Off! I just backed up confout.gro to ./#confout.gro.1# >> Last frame 0 time 2000.000 >> >> however, something is wrong with the trajectory, even tried the xtc, same >> problem there. There seems to be enough frames, but they don't "appear" >> after the s
Re: [gmx-users] trjconv not able to generated output
On 9/8/17 9:47 AM, Sergio Manzetti wrote: I have done this many times before, its doesn't give any problems, it gives the last frame and only that. But not in this case What do you mean? The screen output says it wrote a coordinate file at t=2000 ps. -Justin Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" To: "gmx-users" Sent: Friday, September 8, 2017 3:52:52 PM Subject: Re: [gmx-users] trjconv not able to generated output On 9/8/17 9:38 AM, Sergio Manzetti wrote: Hi, I have tried several ways to get the last frame from the output xtc using gmx trjconv, like: sem@Fjordforsk:/media/sem/HDD3/files/sims/BPRP/5$ gmx trjconv -f traj_c -o confout.gro -b 2000 -e 2000 :-) GROMACS - gmx trjconv, VERSION 5.1.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2015, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx trjconv, VERSION 5.1.2 Executable: /usr/bin/gmx Data prefix: /usr Command line: gmx trjconv -f traj_c -o confout.gro -b 2000 -e 2000 Will write gro: Coordinate file in Gromos-87 format Reading file topol.tpr, VERSION 5.1.2 (single precision) Reading file topol.tpr, VERSION 5.1.2 (single precision) Select group for output Group 0 ( System) has 50510 elements Group 1 ( DNA) has 1333 elements Group 2 ( NA) has 71 elements Group 3 ( CL) has 31 elements Group 4 ( PRB) has 28 elements Group 5 ( Ion) has 102 elements Group 6 ( NA) has 71 elements Group 7 ( CL) has 31 elements Group 8 ( PRB) has 28 elements Group 9 ( Other) has 28 elements Group 10 ( NA) has 71 elements Group 11 ( CL) has 31 elements Group 12 ( PRB) has 28 elements Group 13 ( Water) has 49047 elements Group 14 ( SOL) has 49047 elements Group 15 ( non-Water) has 1463 elements Group 16 ( Water_and_ions) has 49149 elements Select a group: 15 Selected 15: 'non-Water' Reading frame 0 time 2000.000 Precision of traj_c.xtc is 0.001 (nm) Using output precision of 0.001 (nm) Back Off! I just backed up confout.gro to ./#confout.gro.1# Last frame 0 time 2000.000 however, something is wrong with the trajectory, even tried the xtc, same problem there. There seems to be enough frames, but they don't "appear" after the selection of groups. You're telling trjconv to skip everything before 2000 ps with -b 2000, so the program will not report any reading of frames before that time. If there was actually a problem, the program would crash with a fatal error. How can I repair or check a trajectory? gmx check, and it will surely report that everything is fine. -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] trjconv not able to generated output
I have done this many times before, its doesn't give any problems, it gives the last frame and only that. But not in this case Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" To: "gmx-users" Sent: Friday, September 8, 2017 3:52:52 PM Subject: Re: [gmx-users] trjconv not able to generated output On 9/8/17 9:38 AM, Sergio Manzetti wrote: > Hi, I have tried several ways to get the last frame from the output xtc using > gmx trjconv, like: > > sem@Fjordforsk:/media/sem/HDD3/files/sims/BPRP/5$ gmx trjconv -f traj_c -o > confout.gro -b 2000 -e 2000 > :-) GROMACS - gmx trjconv, VERSION 5.1.2 (-: > > GROMACS is written by: > Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar > Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch > Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen > Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner > Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff > Erik Marklund Teemu Murtola Szilard Pall Sander Pronk > Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers > Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf > and the project leaders: > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2015, The GROMACS development team at > Uppsala University, Stockholm University and > the Royal Institute of Technology, Sweden. > check out http://www.gromacs.org for more information. > > GROMACS is free software; you can redistribute it and/or modify it > under the terms of the GNU Lesser General Public License > as published by the Free Software Foundation; either version 2.1 > of the License, or (at your option) any later version. > > GROMACS: gmx trjconv, VERSION 5.1.2 > Executable: /usr/bin/gmx > Data prefix: /usr > Command line: > gmx trjconv -f traj_c -o confout.gro -b 2000 -e 2000 > > Will write gro: Coordinate file in Gromos-87 format > Reading file topol.tpr, VERSION 5.1.2 (single precision) > Reading file topol.tpr, VERSION 5.1.2 (single precision) > Select group for output > Group 0 ( System) has 50510 elements > Group 1 ( DNA) has 1333 elements > Group 2 ( NA) has 71 elements > Group 3 ( CL) has 31 elements > Group 4 ( PRB) has 28 elements > Group 5 ( Ion) has 102 elements > Group 6 ( NA) has 71 elements > Group 7 ( CL) has 31 elements > Group 8 ( PRB) has 28 elements > Group 9 ( Other) has 28 elements > Group 10 ( NA) has 71 elements > Group 11 ( CL) has 31 elements > Group 12 ( PRB) has 28 elements > Group 13 ( Water) has 49047 elements > Group 14 ( SOL) has 49047 elements > Group 15 ( non-Water) has 1463 elements > Group 16 ( Water_and_ions) has 49149 elements > Select a group: 15 > Selected 15: 'non-Water' > Reading frame 0 time 2000.000 > Precision of traj_c.xtc is 0.001 (nm) > Using output precision of 0.001 (nm) > > Back Off! I just backed up confout.gro to ./#confout.gro.1# > Last frame 0 time 2000.000 > > however, something is wrong with the trajectory, even tried the xtc, same > problem there. There seems to be enough frames, but they don't "appear" after > the selection of groups. You're telling trjconv to skip everything before 2000 ps with -b 2000, so the program will not report any reading of frames before that time. If there was actually a problem, the program would crash with a fatal error. > How can I repair or check a trajectory? gmx check, and it will surely report that everything is fine. -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. -- Gromacs Users mailing list * Please search the archive at http://
Re: [gmx-users] trjconv not able to generated output
On 9/8/17 9:38 AM, Sergio Manzetti wrote: Hi, I have tried several ways to get the last frame from the output xtc using gmx trjconv, like: sem@Fjordforsk:/media/sem/HDD3/files/sims/BPRP/5$ gmx trjconv -f traj_c -o confout.gro -b 2000 -e 2000 :-) GROMACS - gmx trjconv, VERSION 5.1.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2015, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx trjconv, VERSION 5.1.2 Executable: /usr/bin/gmx Data prefix: /usr Command line: gmx trjconv -f traj_c -o confout.gro -b 2000 -e 2000 Will write gro: Coordinate file in Gromos-87 format Reading file topol.tpr, VERSION 5.1.2 (single precision) Reading file topol.tpr, VERSION 5.1.2 (single precision) Select group for output Group 0 ( System) has 50510 elements Group 1 ( DNA) has 1333 elements Group 2 ( NA) has 71 elements Group 3 ( CL) has 31 elements Group 4 ( PRB) has 28 elements Group 5 ( Ion) has 102 elements Group 6 ( NA) has 71 elements Group 7 ( CL) has 31 elements Group 8 ( PRB) has 28 elements Group 9 ( Other) has 28 elements Group 10 ( NA) has 71 elements Group 11 ( CL) has 31 elements Group 12 ( PRB) has 28 elements Group 13 ( Water) has 49047 elements Group 14 ( SOL) has 49047 elements Group 15 ( non-Water) has 1463 elements Group 16 ( Water_and_ions) has 49149 elements Select a group: 15 Selected 15: 'non-Water' Reading frame 0 time 2000.000 Precision of traj_c.xtc is 0.001 (nm) Using output precision of 0.001 (nm) Back Off! I just backed up confout.gro to ./#confout.gro.1# Last frame 0 time 2000.000 however, something is wrong with the trajectory, even tried the xtc, same problem there. There seems to be enough frames, but they don't "appear" after the selection of groups. You're telling trjconv to skip everything before 2000 ps with -b 2000, so the program will not report any reading of frames before that time. If there was actually a problem, the program would crash with a fatal error. How can I repair or check a trajectory? gmx check, and it will surely report that everything is fine. -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] Trjconv problem invalid argument
On 2/14/17 1:08 PM, Poncho Arvayo Zatarain wrote: Ok, so should i write trjconv before -ng 3, like gmx_gpu density trjconv -ng 3 -f file.xtc -s file.tpr -o out.xtc -skip 100 or donde write -ng in the command line? There is no invocation of trjconv if you're trying to calculate the density. "gmx trjconv" is a command with its own set of options, while "gmx density" is a different command that calculates the density. You can't mix the two. -Justin Thanks De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se en nombre de Justin Lemkul Enviado: martes, 14 de febrero de 2017 09:53 a. m. Para: gmx-us...@gromacs.org Asunto: Re: [gmx-users] Trjconv problem invalid argument On 2/14/17 12:45 PM, Poncho Arvayo Zatarain wrote: Hello Gromacs users: I want to obtain the density of a system using the command: gmx_gpu density -ng trjconv -f file.xtc -s file.tpr -o out.xtc -skip 100, but the following error appears: Invalid command argument: trjconv. What is wrong with trjconv? I am using gromacs 5.0.3 Nothing is wrong with trjconv, but your command is attempting to execute trjconv as an argument to gmx density -ng, which is complete nonsense. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<http://mackerell.umaryland.edu/~jalemkul> Welcome to my site! - University of Maryland, Baltimore<http://mackerell.umaryland.edu/~jalemkul> mackerell.umaryland.edu Welcome to my site! To learn more about me and the work I am doing, please use the navigation links above. == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! GMX-Users List - Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> www.gromacs.org This is the main discussion forum for users of GROMACS and related software. Subscribe, unsubscribe or change your preferences through gmx-users Admin page. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Mailing Lists - Gromacs<http://www.gromacs.org/Support/Mailing_Lists> www.gromacs.org The three mailing lists (see the menu items on the left) have slightly different purposes, and you might not be interested in subscribing to all of them: * 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.org_gmx-users Info Page - Royal Institute of ...<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> maillist.sys.kth.se gromacs.org_gmx-users -- Discussion list for GROMACS users About gromacs.org_gmx-users -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Trjconv problem invalid argument
Ok, so should i write trjconv before -ng 3, like gmx_gpu density trjconv -ng 3 -f file.xtc -s file.tpr -o out.xtc -skip 100 or donde write -ng in the command line? Thanks De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se en nombre de Justin Lemkul Enviado: martes, 14 de febrero de 2017 09:53 a. m. Para: gmx-us...@gromacs.org Asunto: Re: [gmx-users] Trjconv problem invalid argument On 2/14/17 12:45 PM, Poncho Arvayo Zatarain wrote: > > > Hello Gromacs users: I want to obtain the density of a system using the > command: gmx_gpu density -ng trjconv -f file.xtc -s file.tpr -o out.xtc -skip > 100, but the following error appears: Invalid command argument: trjconv. What > is wrong with trjconv? I am using gromacs 5.0.3 > Nothing is wrong with trjconv, but your command is attempting to execute trjconv as an argument to gmx density -ng, which is complete nonsense. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<http://mackerell.umaryland.edu/~jalemkul> Welcome to my site! - University of Maryland, Baltimore<http://mackerell.umaryland.edu/~jalemkul> mackerell.umaryland.edu Welcome to my site! To learn more about me and the work I am doing, please use the navigation links above. == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! GMX-Users List - Gromacs<http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> www.gromacs.org This is the main discussion forum for users of GROMACS and related software. Subscribe, unsubscribe or change your preferences through gmx-users Admin page. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Mailing Lists - Gromacs<http://www.gromacs.org/Support/Mailing_Lists> www.gromacs.org The three mailing lists (see the menu items on the left) have slightly different purposes, and you might not be interested in subscribing to all of them: * 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.org_gmx-users Info Page - Royal Institute of ...<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> maillist.sys.kth.se gromacs.org_gmx-users -- Discussion list for GROMACS users About gromacs.org_gmx-users -- 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] Trjconv problem invalid argument
On 2/14/17 12:45 PM, Poncho Arvayo Zatarain wrote: Hello Gromacs users: I want to obtain the density of a system using the command: gmx_gpu density -ng trjconv -f file.xtc -s file.tpr -o out.xtc -skip 100, but the following error appears: Invalid command argument: trjconv. What is wrong with trjconv? I am using gromacs 5.0.3 Nothing is wrong with trjconv, but your command is attempting to execute trjconv as an argument to gmx density -ng, which is complete nonsense. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv sampling according to a list of arbitrary times
I don't know how to do exactly what you want to do, but you can at least do this so that trjconv doesn't seek from the beginning of the file, it should speed things up a lot: for t in 1 20 220 620; do let b=$t-10 gmx trjconv -dump $t -b $b ... done Anyway, Mark's suggestion is much better because it will help you to avoid your cluster admins getting mad for you creating millions of small files ;) From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Irem Altan Sent: 02 December 2016 18:00:50 To: gmx-us...@gromacs.org Subject: [gmx-users] trjconv sampling according to a list of arbitrary times Hi, I have a very long simulation and I want to run trjconv on the output to save snapshots from a list of times. For instance if t = [1,20, 220, 620] in ps, I would do: gmx trjconv -f all.trr -s nvt.tpr -dump 1 -o conf1.pdb gmx trjconv -f all.trr -s nvt.tpr -dump 20 -o conf2.pdb gmx trjconv -f all.trr -s nvt.tpr -dump 220 -o conf3.pdb gmx trjconv -f all.trr -s nvt.tpr -dump 620 -o conf4.pdb and then join them with trjcat. This is very easy to do with a script. My problem is, each time I run trjconv, gromacs scans the .trr file from the first frame until the desired frame. So if I want to save 300 such configurations, I have to wait for the file to be read 300 times. Is it possible to do this with a single trjconv command, and somehow provide a list of the times I want to sample, so that gromacs reads the file once and saves the necessary snapshots? Best, Irem -- 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] trjconv sampling according to a list of arbitrary times
Hi, There are some other ways to subsample trajectory files, check out the help text. IIRC you can give it an index file of frame numbers, or something like that. Mark On Fri, 2 Dec 2016 23:01 Irem Altan wrote: > Hi, > > I have a very long simulation and I want to run trjconv on the output to > save snapshots from a list of times. For instance if t = [1,20, 220, 620] > in ps, I would do: > > gmx trjconv -f all.trr -s nvt.tpr -dump 1 -o conf1.pdb > gmx trjconv -f all.trr -s nvt.tpr -dump 20 -o conf2.pdb > gmx trjconv -f all.trr -s nvt.tpr -dump 220 -o conf3.pdb > gmx trjconv -f all.trr -s nvt.tpr -dump 620 -o conf4.pdb > > and then join them with trjcat. This is very easy to do with a script. My > problem is, each time I run trjconv, gromacs scans the .trr file from the > first frame until the desired frame. So if I want to save 300 such > configurations, I have to wait for the file to be read 300 times. > > Is it possible to do this with a single trjconv command, and somehow > provide a list of the times I want to sample, so that gromacs reads the > file once and saves the necessary snapshots? > > Best, > Irem > -- > 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] trjconv
Dear Apramita, Unfortunately, the short answer is that you need to think it through. What is being calculated, and how is the trajectory information affected by trjconv? If you for instance apply trjconv -fit rot+trans prior to RDF calculations, you might influence the results. Kind regards, Erik > On 29 Nov 2016, at 07:36, Apramita Chand wrote: > > Dear Justin,Gregory and Erik, > I'd asked earlier whether trjconv might change calculation of > properties.For diffusion probably, I could avoid applying trjconv before > analysis. For RDF, I checked before and after trjconv, there is a slight > difference in the RDFs. For instance , I'm studying a peptide-water-urea > system . On increasing concentration of urea, before I apply trjconv , the > interaction decreases . After applying trjconv , it increases slightly. > But how do I know for sure whether I should apply it or not? > Say I calculate properties like RDF,RMSD, etc after applying trjconv and > properties like diffusion,lifetimes without trjconv ; would that be right? > My peptide isn't broken or anything . It just seems to be partially out of > the box. > > Please advise. > > > Regards, > Apramita > -- > 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] trjconv
Dear Justin,Gregory and Erik, I'd asked earlier whether trjconv might change calculation of properties.For diffusion probably, I could avoid applying trjconv before analysis. For RDF, I checked before and after trjconv, there is a slight difference in the RDFs. For instance , I'm studying a peptide-water-urea system . On increasing concentration of urea, before I apply trjconv , the interaction decreases . After applying trjconv , it increases slightly. But how do I know for sure whether I should apply it or not? Say I calculate properties like RDF,RMSD, etc after applying trjconv and properties like diffusion,lifetimes without trjconv ; would that be right? My peptide isn't broken or anything . It just seems to be partially out of the box. Please advise. Regards, Apramita -- 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] trjconv
On 9/21/16 8:43 AM, Irem Altan wrote: Hi, Is there a way to write out simulation results with trjconv such that the atoms are in the same order as in the input .pdb file with the same chain/atom names? Trajectories are written in this order already. If you had chain information in the input coordinates, they will be incorporated into the .tpr file and you can produce a coordinate file with that information. No such information is ever stored in a trajectory (because things like atom names, residue names, etc are never stored there, anyway). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv -dump buffer overflow
It happens even with the first frame of the .xtc Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-05-31 19:35 GMT+02:00 Mark Abraham : > Hi, > > It's hard to say. Does it happen with earlier frames? > > Mark > > On Mon, May 30, 2016 at 4:33 PM Marlon Sidore > wrote: > > > Dear Gromacs users, > > > > I'm trying to output frames of my trajectory to individual .gro files and > > have been trying to use trjconv -dump (or -sep, which gives the same > > outcome). > > My system is a martini CG membrane with a protein inside, although I > don't > > think the system is the problem as I could run other tools, or the same > > one, through it (cutting the trajectory is also fine with the very same > > tool). > > > > Once trjconv reaches the appropriate time ... it crashes with a buffer > > overflow. I've attached a small part of the error at the end (not sure if > > the whole error is needed ?). > > The command I'm using is this: > > "gmx trjconv -f vicl.xtc -pbc whole -s vicl.tpr -o frame_dump_0.gro -dump > > 360" > > I'm using Gromacs 5.1 (the trajectory comes from it) - and the error is > > also there with Gromacs 5.1.2. > > > > Thanks in advance > > > > """ > > Back Off! I just backed up frame_dump_0.gro to ./#frame_dump_0.gro.3# > > Reading frame1000 time 360.000 > > Dumping frame at t= 3.6e+06 ps > > *** buffer overflow detected ***: > > /home/ubuntu/progs/gromacs-5.1.2/build/bin/gmx terminated > > === Backtrace: = > > /lib/x86_64-linux-gnu/libc.so.6(+0x7333f)[0x7f70e1e6933f] > > /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f70e1f00ccc] > > ... > > """ > > > > Marlon Sidore > > > > > > PhD Student > > Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) > > CNRS - UMR7255 > > 31, Chemin Joseph Aiguier > > 13402 cedex 20 Marseille > > France > > -- > > 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] trjconv -dump buffer overflow
Hi, It's hard to say. Does it happen with earlier frames? Mark On Mon, May 30, 2016 at 4:33 PM Marlon Sidore wrote: > Dear Gromacs users, > > I'm trying to output frames of my trajectory to individual .gro files and > have been trying to use trjconv -dump (or -sep, which gives the same > outcome). > My system is a martini CG membrane with a protein inside, although I don't > think the system is the problem as I could run other tools, or the same > one, through it (cutting the trajectory is also fine with the very same > tool). > > Once trjconv reaches the appropriate time ... it crashes with a buffer > overflow. I've attached a small part of the error at the end (not sure if > the whole error is needed ?). > The command I'm using is this: > "gmx trjconv -f vicl.xtc -pbc whole -s vicl.tpr -o frame_dump_0.gro -dump > 360" > I'm using Gromacs 5.1 (the trajectory comes from it) - and the error is > also there with Gromacs 5.1.2. > > Thanks in advance > > """ > Back Off! I just backed up frame_dump_0.gro to ./#frame_dump_0.gro.3# > Reading frame1000 time 360.000 > Dumping frame at t= 3.6e+06 ps > *** buffer overflow detected ***: > /home/ubuntu/progs/gromacs-5.1.2/build/bin/gmx terminated > === Backtrace: = > /lib/x86_64-linux-gnu/libc.so.6(+0x7333f)[0x7f70e1e6933f] > /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f70e1f00ccc] > ... > """ > > Marlon Sidore > > > PhD Student > Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) > CNRS - UMR7255 > 31, Chemin Joseph Aiguier > 13402 cedex 20 Marseille > France > -- > 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] trjconv index mismatch
You, my friend, are a genius. All worked, thanks tons. Alex On Mon, Apr 18, 2016 at 5:40 PM, Justin Lemkul wrote: > > > On 4/18/16 7:39 PM, Alex wrote: > >> The atom groups, as they appear in the coordinate input, are: >> >> 1. DNA atoms (labeled DA, DC, etc) >> 2. CNT atoms >> 3. SOL >> 4. Ions >> >> I tried the following (prod.tpr and traj_comp.xtc are the original tpr and >> compressed trajectory, respectively): >> >> step 1: >> gmx convert-tpr -s prod.tpr -o cnt_only.tpr >> selected CNT >> step 2: >> trjconv -f traj_comp.xtc -s cnt_only.tpr -o test.pdb >> >> this last one does not even bother to open the menu, it throws the >> following: >> >> --- >> Program trjconv, VERSION 5.0.5 >> Source code file: >> /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxlib/mtop_util.c, >> line: >> 957 >> >> Software inconsistency error: >> Position restraint coordinates are missing >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> --- >> >> Any thoughts? >> >> > You need to make: > > 1. New .tpr with no restraints > 2. Subset .tpr with just the CNT > > > -Justin > > >> >> On Mon, Apr 18, 2016 at 5:33 PM, Justin Lemkul wrote: >> >> >>> >>> On 4/18/16 7:27 PM, Alex wrote: >>> >>> Yes, there are more atoms in the system, but only 2837 of them are labeled "CNT.' Well, I could share the files with you, of course, but you're running the latest version, aren't you? :) As you might expect, yes. >>> >>> Do the atom numbers of the CNT start from 1, or is there something else >>> listed before it in the coordinates and topology? If that's the case, >>> making a matching .tpr via convert-tpr is the only option. >>> >>> -Justin >>> >>> >>> On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul wrote: >>> > On 4/18/16 7:20 PM, Alex wrote: > > Justin, > >> >> I understand what you're saying, but for the life of me I can't >> understand >> where this discrepancy is coming from, because the input coordinates >> have >> 2837 CNT atoms, and trjconv selector menu lists that number correctly. >> Completely lost here. Are there any alternatives to output (in mdp) >> the >> correct group? >> >> >> Without access to your files, there's nothing else I can really tell >> > you. > Presumably there are more atoms in the system, yes? Your index group > somehow specifies out-of-range atoms. Or maybe trjconv isn't parsing > the > .tpr properly (use convert-tpr to output a matching .tpr that has only > CNT > and try again). I feel like there was an issue with this some time > ago; > 5.0.5 is considered old nowadays so the bug should have been fixed :) > > -Justin > > > Alex > > >> On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul >> wrote: >> >> >> >> On 4/18/16 6:17 PM, Alex wrote: >>> >>> Hi all, >>> >>> I've got a system that includes a group named "CNT" consisting of 2837 atoms. To save space, I am outputting (at a very high rate) a compressed trajectory that contains only that group. The GMX version is 5.0.5. Here's the relevant mdp excerpt: nstxout = 1 nstcomm = 1000 nstxout-compressed = 10 compressed-x-grps = CNT nstvout = 1000 nstfout = 500 nstlog = 100 nstenergy = 500 nstlist = 20 Upon trying to convert the compressed trajectory, after selecting the appropriate group from the menu (CNT, 2837 atoms), I get: command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb output: --- Program trjconv, VERSION 5.0.5 Source code file: /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c, line: 1330 Fatal error: Index[2645] 2838 is larger than the number of atoms in the trajectory file (2837). There is a mismatch in the contents of your -f, -s and/or -n files. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Where's this single-atom discrepancy coming from? Any suggestions? Whatever you selected as output contains more atoms than are in the trajectory. Note that it's not necessarily a single-atom >>> discrepancy, >>> it's >>> just that the fatal error is trigg
Re: [gmx-users] trjconv index mismatch
On 4/18/16 7:39 PM, Alex wrote: The atom groups, as they appear in the coordinate input, are: 1. DNA atoms (labeled DA, DC, etc) 2. CNT atoms 3. SOL 4. Ions I tried the following (prod.tpr and traj_comp.xtc are the original tpr and compressed trajectory, respectively): step 1: gmx convert-tpr -s prod.tpr -o cnt_only.tpr selected CNT step 2: trjconv -f traj_comp.xtc -s cnt_only.tpr -o test.pdb this last one does not even bother to open the menu, it throws the following: --- Program trjconv, VERSION 5.0.5 Source code file: /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxlib/mtop_util.c, line: 957 Software inconsistency error: Position restraint coordinates are missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Any thoughts? You need to make: 1. New .tpr with no restraints 2. Subset .tpr with just the CNT -Justin On Mon, Apr 18, 2016 at 5:33 PM, Justin Lemkul wrote: On 4/18/16 7:27 PM, Alex wrote: Yes, there are more atoms in the system, but only 2837 of them are labeled "CNT.' Well, I could share the files with you, of course, but you're running the latest version, aren't you? :) As you might expect, yes. Do the atom numbers of the CNT start from 1, or is there something else listed before it in the coordinates and topology? If that's the case, making a matching .tpr via convert-tpr is the only option. -Justin On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul wrote: On 4/18/16 7:20 PM, Alex wrote: Justin, I understand what you're saying, but for the life of me I can't understand where this discrepancy is coming from, because the input coordinates have 2837 CNT atoms, and trjconv selector menu lists that number correctly. Completely lost here. Are there any alternatives to output (in mdp) the correct group? Without access to your files, there's nothing else I can really tell you. Presumably there are more atoms in the system, yes? Your index group somehow specifies out-of-range atoms. Or maybe trjconv isn't parsing the .tpr properly (use convert-tpr to output a matching .tpr that has only CNT and try again). I feel like there was an issue with this some time ago; 5.0.5 is considered old nowadays so the bug should have been fixed :) -Justin Alex On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul wrote: On 4/18/16 6:17 PM, Alex wrote: Hi all, I've got a system that includes a group named "CNT" consisting of 2837 atoms. To save space, I am outputting (at a very high rate) a compressed trajectory that contains only that group. The GMX version is 5.0.5. Here's the relevant mdp excerpt: nstxout = 1 nstcomm = 1000 nstxout-compressed = 10 compressed-x-grps = CNT nstvout = 1000 nstfout = 500 nstlog = 100 nstenergy = 500 nstlist = 20 Upon trying to convert the compressed trajectory, after selecting the appropriate group from the menu (CNT, 2837 atoms), I get: command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb output: --- Program trjconv, VERSION 5.0.5 Source code file: /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c, line: 1330 Fatal error: Index[2645] 2838 is larger than the number of atoms in the trajectory file (2837). There is a mismatch in the contents of your -f, -s and/or -n files. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Where's this single-atom discrepancy coming from? Any suggestions? Whatever you selected as output contains more atoms than are in the trajectory. Note that it's not necessarily a single-atom discrepancy, it's just that the fatal error is triggered as soon as an index that is out of range is identified. You're only outputting CNT, and presumably the .tpr contains more atoms, so the selection you're making can only be CNT or some subset of those atoms. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv index mismatch
The atom groups, as they appear in the coordinate input, are: 1. DNA atoms (labeled DA, DC, etc) 2. CNT atoms 3. SOL 4. Ions I tried the following (prod.tpr and traj_comp.xtc are the original tpr and compressed trajectory, respectively): step 1: gmx convert-tpr -s prod.tpr -o cnt_only.tpr selected CNT step 2: trjconv -f traj_comp.xtc -s cnt_only.tpr -o test.pdb this last one does not even bother to open the menu, it throws the following: --- Program trjconv, VERSION 5.0.5 Source code file: /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxlib/mtop_util.c, line: 957 Software inconsistency error: Position restraint coordinates are missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Any thoughts? On Mon, Apr 18, 2016 at 5:33 PM, Justin Lemkul wrote: > > > On 4/18/16 7:27 PM, Alex wrote: > >> Yes, there are more atoms in the system, but only 2837 of them are labeled >> "CNT.' Well, I could share the files with you, of course, but you're >> running the latest version, aren't you? :) >> >> > As you might expect, yes. > > Do the atom numbers of the CNT start from 1, or is there something else > listed before it in the coordinates and topology? If that's the case, > making a matching .tpr via convert-tpr is the only option. > > -Justin > > > On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul wrote: >> >> >>> >>> On 4/18/16 7:20 PM, Alex wrote: >>> >>> Justin, I understand what you're saying, but for the life of me I can't understand where this discrepancy is coming from, because the input coordinates have 2837 CNT atoms, and trjconv selector menu lists that number correctly. Completely lost here. Are there any alternatives to output (in mdp) the correct group? Without access to your files, there's nothing else I can really tell >>> you. >>> Presumably there are more atoms in the system, yes? Your index group >>> somehow specifies out-of-range atoms. Or maybe trjconv isn't parsing the >>> .tpr properly (use convert-tpr to output a matching .tpr that has only >>> CNT >>> and try again). I feel like there was an issue with this some time ago; >>> 5.0.5 is considered old nowadays so the bug should have been fixed :) >>> >>> -Justin >>> >>> >>> Alex >>> On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul wrote: > On 4/18/16 6:17 PM, Alex wrote: > > Hi all, > >> >> I've got a system that includes a group named "CNT" consisting of 2837 >> atoms. To save space, I am outputting (at a very high rate) a >> compressed >> trajectory that contains only that group. The GMX version is 5.0.5. >> Here's >> the relevant mdp excerpt: >> >> >> nstxout = 1 >> nstcomm = 1000 >> nstxout-compressed = 10 >> compressed-x-grps = CNT >> nstvout = 1000 >> nstfout = 500 >> nstlog = 100 >> nstenergy = 500 >> nstlist = 20 >> >> Upon trying to convert the compressed trajectory, after selecting the >> appropriate group from the menu (CNT, 2837 atoms), I get: >> >> command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb >> >> output: >> --- >> Program trjconv, VERSION 5.0.5 >> Source code file: >> >> /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c, >> line: 1330 >> >> Fatal error: >> Index[2645] 2838 is larger than the number of atoms in the >> trajectory file (2837). There is a mismatch in the contents >> of your -f, -s and/or -n files. >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> Where's this single-atom discrepancy coming from? Any suggestions? >> >> >> Whatever you selected as output contains more atoms than are in the >> > trajectory. Note that it's not necessarily a single-atom discrepancy, > it's > just that the fatal error is triggered as soon as an index that is out > of > range is identified. You're only outputting CNT, and presumably the > .tpr > contains more atoms, so the selection you're making can only be CNT or > some > subset of those atoms. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.u
Re: [gmx-users] trjconv index mismatch
On 4/18/16 7:27 PM, Alex wrote: Yes, there are more atoms in the system, but only 2837 of them are labeled "CNT.' Well, I could share the files with you, of course, but you're running the latest version, aren't you? :) As you might expect, yes. Do the atom numbers of the CNT start from 1, or is there something else listed before it in the coordinates and topology? If that's the case, making a matching .tpr via convert-tpr is the only option. -Justin On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul wrote: On 4/18/16 7:20 PM, Alex wrote: Justin, I understand what you're saying, but for the life of me I can't understand where this discrepancy is coming from, because the input coordinates have 2837 CNT atoms, and trjconv selector menu lists that number correctly. Completely lost here. Are there any alternatives to output (in mdp) the correct group? Without access to your files, there's nothing else I can really tell you. Presumably there are more atoms in the system, yes? Your index group somehow specifies out-of-range atoms. Or maybe trjconv isn't parsing the .tpr properly (use convert-tpr to output a matching .tpr that has only CNT and try again). I feel like there was an issue with this some time ago; 5.0.5 is considered old nowadays so the bug should have been fixed :) -Justin Alex On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul wrote: On 4/18/16 6:17 PM, Alex wrote: Hi all, I've got a system that includes a group named "CNT" consisting of 2837 atoms. To save space, I am outputting (at a very high rate) a compressed trajectory that contains only that group. The GMX version is 5.0.5. Here's the relevant mdp excerpt: nstxout = 1 nstcomm = 1000 nstxout-compressed = 10 compressed-x-grps = CNT nstvout = 1000 nstfout = 500 nstlog = 100 nstenergy = 500 nstlist = 20 Upon trying to convert the compressed trajectory, after selecting the appropriate group from the menu (CNT, 2837 atoms), I get: command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb output: --- Program trjconv, VERSION 5.0.5 Source code file: /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c, line: 1330 Fatal error: Index[2645] 2838 is larger than the number of atoms in the trajectory file (2837). There is a mismatch in the contents of your -f, -s and/or -n files. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Where's this single-atom discrepancy coming from? Any suggestions? Whatever you selected as output contains more atoms than are in the trajectory. Note that it's not necessarily a single-atom discrepancy, it's just that the fatal error is triggered as soon as an index that is out of range is identified. You're only outputting CNT, and presumably the .tpr contains more atoms, so the selection you're making can only be CNT or some subset of those atoms. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 h
Re: [gmx-users] trjconv index mismatch
Yes, there are more atoms in the system, but only 2837 of them are labeled "CNT.' Well, I could share the files with you, of course, but you're running the latest version, aren't you? :) On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul wrote: > > > On 4/18/16 7:20 PM, Alex wrote: > >> Justin, >> >> I understand what you're saying, but for the life of me I can't understand >> where this discrepancy is coming from, because the input coordinates have >> 2837 CNT atoms, and trjconv selector menu lists that number correctly. >> Completely lost here. Are there any alternatives to output (in mdp) the >> correct group? >> >> > Without access to your files, there's nothing else I can really tell you. > Presumably there are more atoms in the system, yes? Your index group > somehow specifies out-of-range atoms. Or maybe trjconv isn't parsing the > .tpr properly (use convert-tpr to output a matching .tpr that has only CNT > and try again). I feel like there was an issue with this some time ago; > 5.0.5 is considered old nowadays so the bug should have been fixed :) > > -Justin > > > Alex >> >> On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul wrote: >> >> >>> >>> On 4/18/16 6:17 PM, Alex wrote: >>> >>> Hi all, I've got a system that includes a group named "CNT" consisting of 2837 atoms. To save space, I am outputting (at a very high rate) a compressed trajectory that contains only that group. The GMX version is 5.0.5. Here's the relevant mdp excerpt: nstxout = 1 nstcomm = 1000 nstxout-compressed = 10 compressed-x-grps = CNT nstvout = 1000 nstfout = 500 nstlog = 100 nstenergy = 500 nstlist = 20 Upon trying to convert the compressed trajectory, after selecting the appropriate group from the menu (CNT, 2837 atoms), I get: command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb output: --- Program trjconv, VERSION 5.0.5 Source code file: /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c, line: 1330 Fatal error: Index[2645] 2838 is larger than the number of atoms in the trajectory file (2837). There is a mismatch in the contents of your -f, -s and/or -n files. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Where's this single-atom discrepancy coming from? Any suggestions? Whatever you selected as output contains more atoms than are in the >>> trajectory. Note that it's not necessarily a single-atom discrepancy, >>> it's >>> just that the fatal error is triggered as soon as an index that is out of >>> range is identified. You're only outputting CNT, and presumably the .tpr >>> contains more atoms, so the selection you're making can only be CNT or >>> some >>> subset of those atoms. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> == >>> -- >>> 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. >>> >>> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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?
Re: [gmx-users] trjconv index mismatch
On 4/18/16 7:20 PM, Alex wrote: Justin, I understand what you're saying, but for the life of me I can't understand where this discrepancy is coming from, because the input coordinates have 2837 CNT atoms, and trjconv selector menu lists that number correctly. Completely lost here. Are there any alternatives to output (in mdp) the correct group? Without access to your files, there's nothing else I can really tell you. Presumably there are more atoms in the system, yes? Your index group somehow specifies out-of-range atoms. Or maybe trjconv isn't parsing the .tpr properly (use convert-tpr to output a matching .tpr that has only CNT and try again). I feel like there was an issue with this some time ago; 5.0.5 is considered old nowadays so the bug should have been fixed :) -Justin Alex On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul wrote: On 4/18/16 6:17 PM, Alex wrote: Hi all, I've got a system that includes a group named "CNT" consisting of 2837 atoms. To save space, I am outputting (at a very high rate) a compressed trajectory that contains only that group. The GMX version is 5.0.5. Here's the relevant mdp excerpt: nstxout = 1 nstcomm = 1000 nstxout-compressed = 10 compressed-x-grps = CNT nstvout = 1000 nstfout = 500 nstlog = 100 nstenergy = 500 nstlist = 20 Upon trying to convert the compressed trajectory, after selecting the appropriate group from the menu (CNT, 2837 atoms), I get: command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb output: --- Program trjconv, VERSION 5.0.5 Source code file: /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c, line: 1330 Fatal error: Index[2645] 2838 is larger than the number of atoms in the trajectory file (2837). There is a mismatch in the contents of your -f, -s and/or -n files. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Where's this single-atom discrepancy coming from? Any suggestions? Whatever you selected as output contains more atoms than are in the trajectory. Note that it's not necessarily a single-atom discrepancy, it's just that the fatal error is triggered as soon as an index that is out of range is identified. You're only outputting CNT, and presumably the .tpr contains more atoms, so the selection you're making can only be CNT or some subset of those atoms. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv index mismatch
Justin, I understand what you're saying, but for the life of me I can't understand where this discrepancy is coming from, because the input coordinates have 2837 CNT atoms, and trjconv selector menu lists that number correctly. Completely lost here. Are there any alternatives to output (in mdp) the correct group? Alex On Mon, Apr 18, 2016 at 5:15 PM, Justin Lemkul wrote: > > > On 4/18/16 6:17 PM, Alex wrote: > >> Hi all, >> >> I've got a system that includes a group named "CNT" consisting of 2837 >> atoms. To save space, I am outputting (at a very high rate) a compressed >> trajectory that contains only that group. The GMX version is 5.0.5. Here's >> the relevant mdp excerpt: >> >> >> nstxout = 1 >> nstcomm = 1000 >> nstxout-compressed = 10 >> compressed-x-grps = CNT >> nstvout = 1000 >> nstfout = 500 >> nstlog = 100 >> nstenergy = 500 >> nstlist = 20 >> >> Upon trying to convert the compressed trajectory, after selecting the >> appropriate group from the menu (CNT, 2837 atoms), I get: >> >> command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb >> >> output: >> --- >> Program trjconv, VERSION 5.0.5 >> Source code file: >> /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c, >> line: 1330 >> >> Fatal error: >> Index[2645] 2838 is larger than the number of atoms in the >> trajectory file (2837). There is a mismatch in the contents >> of your -f, -s and/or -n files. >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> Where's this single-atom discrepancy coming from? Any suggestions? >> >> > Whatever you selected as output contains more atoms than are in the > trajectory. Note that it's not necessarily a single-atom discrepancy, it's > just that the fatal error is triggered as soon as an index that is out of > range is identified. You're only outputting CNT, and presumably the .tpr > contains more atoms, so the selection you're making can only be CNT or some > subset of those atoms. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] trjconv index mismatch
On 4/18/16 6:17 PM, Alex wrote: Hi all, I've got a system that includes a group named "CNT" consisting of 2837 atoms. To save space, I am outputting (at a very high rate) a compressed trajectory that contains only that group. The GMX version is 5.0.5. Here's the relevant mdp excerpt: nstxout = 1 nstcomm = 1000 nstxout-compressed = 10 compressed-x-grps = CNT nstvout = 1000 nstfout = 500 nstlog = 100 nstenergy = 500 nstlist = 20 Upon trying to convert the compressed trajectory, after selecting the appropriate group from the menu (CNT, 2837 atoms), I get: command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb output: --- Program trjconv, VERSION 5.0.5 Source code file: /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c, line: 1330 Fatal error: Index[2645] 2838 is larger than the number of atoms in the trajectory file (2837). There is a mismatch in the contents of your -f, -s and/or -n files. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Where's this single-atom discrepancy coming from? Any suggestions? Whatever you selected as output contains more atoms than are in the trajectory. Note that it's not necessarily a single-atom discrepancy, it's just that the fatal error is triggered as soon as an index that is out of range is identified. You're only outputting CNT, and presumably the .tpr contains more atoms, so the selection you're making can only be CNT or some subset of those atoms. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv index mismatch
Dear all, is there an international workshop about Gromacs in America or Europe the near future?. 2016-04-18 17:17 GMT-05:00 Alex : > Hi all, > > I've got a system that includes a group named "CNT" consisting of 2837 > atoms. To save space, I am outputting (at a very high rate) a compressed > trajectory that contains only that group. The GMX version is 5.0.5. Here's > the relevant mdp excerpt: > > > nstxout = 1 > nstcomm = 1000 > nstxout-compressed = 10 > compressed-x-grps = CNT > nstvout = 1000 > nstfout = 500 > nstlog = 100 > nstenergy = 500 > nstlist = 20 > > Upon trying to convert the compressed trajectory, after selecting the > appropriate group from the menu (CNT, 2837 atoms), I get: > > command: trjconv -f traj_comp.xtc -s prod.tpr -o test.pdb > > output: > --- > Program trjconv, VERSION 5.0.5 > Source code file: > /home/smolyan/Downloads/gromacs-5.0.5/src/gromacs/gmxana/gmx_trjconv.c, > line: 1330 > > Fatal error: > Index[2645] 2838 is larger than the number of atoms in the > trajectory file (2837). There is a mismatch in the contents > of your -f, -s and/or -n files. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > Where's this single-atom discrepancy coming from? Any suggestions? > > Thanks, > > Alex > -- > 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. > -- Juan Manuel Aceves Hernández Laboratorio de Nanomateriales Tel. 52 55 5623 1999 ext 39431 Tel y Fax 5623 20 68 Unidad de Investigación Multidisciplinaria Campo 4, Facultad de Estudios Superiores Cuautitlan Universidad Nacional Autonoma de México -- 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] trjconv options?
On 2/4/16 4:27 AM, Timofey Tyugashev wrote: Message: 2 Date: Wed, 3 Feb 2016 07:37:42 -0500 From: Justin Lemkul To:gmx-us...@gromacs.org Subject: Re: [gmx-users] trjconv options? Message-ID:<56b1f496.5090...@vt.edu> Content-Type: text/plain; charset=windows-1252; format=flowed On 2/3/16 6:34 AM, Timofey Tyugashev wrote: >Thank you for replies on my previous questions. >And now I have another one dealing with trjconv. > >I have a simulation of a three-chain protein/nucleic acid complex. Naturally, >it gets broken in three separate strands by PBC. >After trying several, I settled on using options '-pbc mol' with '-ur compact' >which makes the complex look decent again and it looks like that does the job. >But I'm worried about a possibility of something getting unrepaired by this >option and getting unnoticed by me. What is the way to check for it? Any molecules that appear to fly away suddenly will be a pretty dead giveaway. In general, for multimeric complexes, you need to do a lot more work, e.g. centering on a single chain after making molecules whole and removing jumps. If a simple -pbc mol -ur compact does the trick, probably nothing has actually crossed a periodic boundary yet. >Also it keeps tumbling around the cell during the trajectory. It's annoying. Is >there a way to pin down the cluster and stop it from rotating? This is what trjconv -fit is for. -Justin Well, both vmd and pymol render .gro file (and trajectory files) with DNA strands and protein positioned in different corners of the box. Also, editconf -pbc has no effect on .gro file with the broken complex. How it's supposed to behave? So in this case I should at first run trjconv with '-pbc whole', make second run with '-pbc nojump', then make third run with '-pbc mol' to properly repair the trajectory? I guess for -fit I should pick 'progressive' option? Complex systems require complex operations. Start with http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow because that order of operations generally works well. Then see posts in the archive, because this comes up frequently. Typically, after making molecules whole and removing jumps, you can center on a custom index group that defines some useful center. Then you can do whatever fitting you like. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv options?
Message: 2 Date: Wed, 3 Feb 2016 07:37:42 -0500 From: Justin Lemkul To:gmx-us...@gromacs.org Subject: Re: [gmx-users] trjconv options? Message-ID:<56b1f496.5090...@vt.edu> Content-Type: text/plain; charset=windows-1252; format=flowed On 2/3/16 6:34 AM, Timofey Tyugashev wrote: >Thank you for replies on my previous questions. >And now I have another one dealing with trjconv. > >I have a simulation of a three-chain protein/nucleic acid complex. Naturally, >it gets broken in three separate strands by PBC. >After trying several, I settled on using options '-pbc mol' with '-ur compact' >which makes the complex look decent again and it looks like that does the job. >But I'm worried about a possibility of something getting unrepaired by this >option and getting unnoticed by me. What is the way to check for it? Any molecules that appear to fly away suddenly will be a pretty dead giveaway. In general, for multimeric complexes, you need to do a lot more work, e.g. centering on a single chain after making molecules whole and removing jumps. If a simple -pbc mol -ur compact does the trick, probably nothing has actually crossed a periodic boundary yet. >Also it keeps tumbling around the cell during the trajectory. It's annoying. Is >there a way to pin down the cluster and stop it from rotating? This is what trjconv -fit is for. -Justin Well, both vmd and pymol render .gro file (and trajectory files) with DNA strands and protein positioned in different corners of the box. Also, editconf -pbc has no effect on .gro file with the broken complex. How it's supposed to behave? So in this case I should at first run trjconv with '-pbc whole', make second run with '-pbc nojump', then make third run with '-pbc mol' to properly repair the trajectory? I guess for -fit I should pick 'progressive' option? -- 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] trjconv options?
On 2/3/16 6:34 AM, Timofey Tyugashev wrote: Thank you for replies on my previous questions. And now I have another one dealing with trjconv. I have a simulation of a three-chain protein/nucleic acid complex. Naturally, it gets broken in three separate strands by PBC. After trying several, I settled on using options '-pbc mol' with '-ur compact' which makes the complex look decent again and it looks like that does the job. But I'm worried about a possibility of something getting unrepaired by this option and getting unnoticed by me. What is the way to check for it? Any molecules that appear to fly away suddenly will be a pretty dead giveaway. In general, for multimeric complexes, you need to do a lot more work, e.g. centering on a single chain after making molecules whole and removing jumps. If a simple -pbc mol -ur compact does the trick, probably nothing has actually crossed a periodic boundary yet. Also it keeps tumbling around the cell during the trajectory. It's annoying. Is there a way to pin down the cluster and stop it from rotating? This is what trjconv -fit is for. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv - two chains are separated
I have also encountered this problem and was able to solve it using the tpr file generated before running editconf as the input to trjconv (with -pbc no jump). Peter Sent from my iPad > On 3 בפבר׳ 2016, at 4:51, Catarina A. Carvalheda dos Santos > wrote: > > Hi there, > > I had similar problems in the past. You'll have to play with trjconv and > find the best combination of different flags to solve the visualization > problem. > > You can start by trying out this workflow for example: > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > Hope this helps. > > Good luck! > > > > On 3 February 2016 at 06:15, Trayder Thomas > wrote: > >> For "-pbc nojump" to work, you need to make sure they are together (as you >> want) in the first frame of your input trajectory. >> >> The most reliable way to do this is by centering the trajectory on a >> residue at the interface between the two chains (using a custom index >> group). >> >> I've also heard some people have had luck with "-pbc cluster" >> >> You can then run "-pbc nojump" on the centered (or clustered) trajectory. >> >> -Trayder >> >> >> >> >>> On Wed, Feb 3, 2016 at 9:37 AM, Yunlong Liu wrote: >>> >>> Hi Gromacs Users, >>> >>> I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my >> trajectories. >>> My protein has two chains (A and B) and they closely bind to each other. >>> after running trjconv with "-pbc nojump", two chains are greatly >> separated >>> by a certain distance. It is mostly likely that the pbc is not >> successfully >>> removed and the program takes a chain from one unit cell and another from >>> another unit cell. >>> >>> Does anybody have any idea to solve the problem? >>> >>> Best >>> Yunlong >>> -- >>> 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. >> >> The University of Dundee is a registered Scottish Charity, No: SC015096 > > > > -- > Catarina A. Carvalheda > > PhD Student > Computational Biology Division > SLS & SSE > University of Dundee > DD1 5EH, Dundee, Scotland, UK > -- > 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] trjconv - two chains are separated
Hi there, I had similar problems in the past. You'll have to play with trjconv and find the best combination of different flags to solve the visualization problem. You can start by trying out this workflow for example: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Hope this helps. Good luck! On 3 February 2016 at 06:15, Trayder Thomas wrote: > For "-pbc nojump" to work, you need to make sure they are together (as you > want) in the first frame of your input trajectory. > > The most reliable way to do this is by centering the trajectory on a > residue at the interface between the two chains (using a custom index > group). > > I've also heard some people have had luck with "-pbc cluster" > > You can then run "-pbc nojump" on the centered (or clustered) trajectory. > > -Trayder > > > > > On Wed, Feb 3, 2016 at 9:37 AM, Yunlong Liu wrote: > > > Hi Gromacs Users, > > > > I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my > trajectories. > > My protein has two chains (A and B) and they closely bind to each other. > > after running trjconv with "-pbc nojump", two chains are greatly > separated > > by a certain distance. It is mostly likely that the pbc is not > successfully > > removed and the program takes a chain from one unit cell and another from > > another unit cell. > > > > Does anybody have any idea to solve the problem? > > > > Best > > Yunlong > > -- > > 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. > > The University of Dundee is a registered Scottish Charity, No: SC015096 > -- Catarina A. Carvalheda PhD Student Computational Biology Division SLS & SSE University of Dundee DD1 5EH, Dundee, Scotland, UK -- 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] trjconv - two chains are separated
For "-pbc nojump" to work, you need to make sure they are together (as you want) in the first frame of your input trajectory. The most reliable way to do this is by centering the trajectory on a residue at the interface between the two chains (using a custom index group). I've also heard some people have had luck with "-pbc cluster" You can then run "-pbc nojump" on the centered (or clustered) trajectory. -Trayder On Wed, Feb 3, 2016 at 9:37 AM, Yunlong Liu wrote: > Hi Gromacs Users, > > I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my trajectories. > My protein has two chains (A and B) and they closely bind to each other. > after running trjconv with "-pbc nojump", two chains are greatly separated > by a certain distance. It is mostly likely that the pbc is not successfully > removed and the program takes a chain from one unit cell and another from > another unit cell. > > Does anybody have any idea to solve the problem? > > Best > Yunlong > -- > 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] trjconv -pbc nojump
Thanks, I found that there is an option -nojump also for g_traj, which I use to get the average height. That solves the problem for my purpose. Cheers Sabine -- Dr. Sabine Reißer Theoretical Chemical Biology Institute of Physical Chemistry Karlsruhe Institute of Technology Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se im Auftrag von Justin Lemkul Gesendet: Mittwoch, 2. September 2015 22:40 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] trjconv -pbc nojump On 9/2/15 9:36 AM, Reisser, Sabine (IPC) wrote: > Well, in the end I would like to have an average value for the P atoms of > each leaflet. I know which lipids belong to which leaflet, but I need to > avoid box jumps along z, otherwise I will obviously get a wrong average. > Using first trjconv -pbc whole and then -pbc nojump actually seems to work > in the way that molecules don't jump in z anymore. However, they are not > whole anymore. Also, I would like all lipids of one leaflet on one side of Once made whole, I don't understand how they would have further problems. Make sure your reference structure in the .tpr passed to -s has whole molecules that are all in the box as a proper reference. > the box. Now, the lipids upper edge is at the box edge, and some have jumped > to the lower box edge. I thought maybe with -pbc cluster I could fix this. > Otherwise I have to shift the molecules which are jumped (already in the > starting structure) manually by the box height. > This can be overcome with the -trans (in concert with -pbc mol) and/or -center options. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv -pbc nojump
On 9/2/15 9:36 AM, Reisser, Sabine (IPC) wrote: Well, in the end I would like to have an average value for the P atoms of each leaflet. I know which lipids belong to which leaflet, but I need to avoid box jumps along z, otherwise I will obviously get a wrong average. Using first trjconv -pbc whole and then -pbc nojump actually seems to work in the way that molecules don't jump in z anymore. However, they are not whole anymore. Also, I would like all lipids of one leaflet on one side of Once made whole, I don't understand how they would have further problems. Make sure your reference structure in the .tpr passed to -s has whole molecules that are all in the box as a proper reference. the box. Now, the lipids upper edge is at the box edge, and some have jumped to the lower box edge. I thought maybe with -pbc cluster I could fix this. Otherwise I have to shift the molecules which are jumped (already in the starting structure) manually by the box height. This can be overcome with the -trans (in concert with -pbc mol) and/or -center options. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv -pbc nojump
Well, in the end I would like to have an average value for the P atoms of each leaflet. I know which lipids belong to which leaflet, but I need to avoid box jumps along z, otherwise I will obviously get a wrong average. Using first trjconv -pbc whole and then -pbc nojump actually seems to work in the way that molecules don't jump in z anymore. However, they are not whole anymore. Also, I would like all lipids of one leaflet on one side of the box. Now, the lipids upper edge is at the box edge, and some have jumped to the lower box edge. I thought maybe with -pbc cluster I could fix this. Otherwise I have to shift the molecules which are jumped (already in the starting structure) manually by the box height. Cheers Sabine -- Dr. Sabine Reißer Theoretical Chemical Biology Institute of Physical Chemistry Karlsruhe Institute of Technology Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se im Auftrag von Justin Lemkul Gesendet: Mittwoch, 2. September 2015 15:06 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] trjconv -pbc nojump On 9/2/15 9:04 AM, Reisser, Sabine (IPC) wrote: > Thanks, I made them whole and tried to cluster the lipids with -pbc cluster. > However, I keep getting a Fatal error: > Molecule 1 marked for clustering but not atom 1 in it - check your index! > > This happens no matter which index group I use. > Do you have any ideas what's the reason? > Does it even make sense to try to cluster these molecules? Note that not every step on that list is needed. -Justin > Cheers > Sabine > > > -- > Dr. Sabine Reißer > Theoretical Chemical Biology > Institute of Physical Chemistry > Karlsruhe Institute of Technology > > > > Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > im Auftrag von Justin > Lemkul > Gesendet: Mittwoch, 2. September 2015 14:13 > An: gmx-us...@gromacs.org > Betreff: Re: [gmx-users] trjconv -pbc nojump > > On 9/2/15 7:17 AM, Reisser, Sabine (IPC) wrote: >> Thanks for the reply, but I don't want the lipids to jump from one edge of >> the box to the other, which they do with this option, even though they >> remain complete. >> > > Making molecules whole should be the first step, followed by removing jumps. > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow > > -Justin > >> Cheers >> Sabine >> >> >> >> -- >> Dr. Sabine Reißer >> Theoretical Chemical Biology >> Institute of Physical Chemistry >> Karlsruhe Institute of Technology >> >> >> ________________ >> Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> im Auftrag von Ganesh >> Shahane >> Gesendet: Mittwoch, 2. September 2015 12:19 >> An: gmx-us...@gromacs.org >> Betreff: Re: [gmx-users] trjconv -pbc nojump >> >> Hi Reisser, >> >> Instead of using -pbc nojump, use -pbc whole. >> >> On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) < >> sabine.reis...@kit.edu> wrote: >> >>> Hi, >>> >>> >>> I want to use trjconv -pbc nojump to create a trajectory without box >>> jumping of molecules. The molecules (lipids) also start to diffuse out of >>> the box like they should, but in some a part of the molecule still jumps >>> (as I could observe in xy direction), while the rest doesn't, leading to >>> artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr >>> file in the -s option, or a gro file (with only complete molecules), same >>> result. >>> >>> >>> I'd be glad if somebody could give me a hint. >>> >>> >>> Cheers >>> >>> Sabine >>> >>> >>> >>> -- >>> Dr. Sabine Reißer >>> Theoretical Chemical Biology >>> Institute of Physical Chemistry >>> Karlsruhe Institute of Technology >>> >>> -- >>> 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. >>> >> >> >> >> -- >> Best Regards, >> Ganesh Shahane >> -- >> Gromacs Users mailing list >> >> * Please se
Re: [gmx-users] trjconv -pbc nojump
On 9/2/15 9:04 AM, Reisser, Sabine (IPC) wrote: Thanks, I made them whole and tried to cluster the lipids with -pbc cluster. However, I keep getting a Fatal error: Molecule 1 marked for clustering but not atom 1 in it - check your index! This happens no matter which index group I use. Do you have any ideas what's the reason? Does it even make sense to try to cluster these molecules? Note that not every step on that list is needed. -Justin Cheers Sabine -- Dr. Sabine Reißer Theoretical Chemical Biology Institute of Physical Chemistry Karlsruhe Institute of Technology Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se im Auftrag von Justin Lemkul Gesendet: Mittwoch, 2. September 2015 14:13 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] trjconv -pbc nojump On 9/2/15 7:17 AM, Reisser, Sabine (IPC) wrote: Thanks for the reply, but I don't want the lipids to jump from one edge of the box to the other, which they do with this option, even though they remain complete. Making molecules whole should be the first step, followed by removing jumps. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -Justin Cheers Sabine -- Dr. Sabine Reißer Theoretical Chemical Biology Institute of Physical Chemistry Karlsruhe Institute of Technology Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se im Auftrag von Ganesh Shahane Gesendet: Mittwoch, 2. September 2015 12:19 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] trjconv -pbc nojump Hi Reisser, Instead of using -pbc nojump, use -pbc whole. On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) < sabine.reis...@kit.edu> wrote: Hi, I want to use trjconv -pbc nojump to create a trajectory without box jumping of molecules. The molecules (lipids) also start to diffuse out of the box like they should, but in some a part of the molecule still jumps (as I could observe in xy direction), while the rest doesn't, leading to artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr file in the -s option, or a gro file (with only complete molecules), same result. I'd be glad if somebody could give me a hint. Cheers Sabine -- Dr. Sabine Reißer Theoretical Chemical Biology Institute of Physical Chemistry Karlsruhe Institute of Technology -- 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. -- Best Regards, Ganesh Shahane -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv -pbc nojump
Thanks, I made them whole and tried to cluster the lipids with -pbc cluster. However, I keep getting a Fatal error: Molecule 1 marked for clustering but not atom 1 in it - check your index! This happens no matter which index group I use. Do you have any ideas what's the reason? Cheers Sabine -- Dr. Sabine Reißer Theoretical Chemical Biology Institute of Physical Chemistry Karlsruhe Institute of Technology Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se im Auftrag von Justin Lemkul Gesendet: Mittwoch, 2. September 2015 14:13 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] trjconv -pbc nojump On 9/2/15 7:17 AM, Reisser, Sabine (IPC) wrote: > Thanks for the reply, but I don't want the lipids to jump from one edge of > the box to the other, which they do with this option, even though they remain > complete. > Making molecules whole should be the first step, followed by removing jumps. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -Justin > Cheers > Sabine > > > > -- > Dr. Sabine Reißer > Theoretical Chemical Biology > Institute of Physical Chemistry > Karlsruhe Institute of Technology > > > > Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > im Auftrag von Ganesh > Shahane > Gesendet: Mittwoch, 2. September 2015 12:19 > An: gmx-us...@gromacs.org > Betreff: Re: [gmx-users] trjconv -pbc nojump > > Hi Reisser, > > Instead of using -pbc nojump, use -pbc whole. > > On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) < > sabine.reis...@kit.edu> wrote: > >> Hi, >> >> >> I want to use trjconv -pbc nojump to create a trajectory without box >> jumping of molecules. The molecules (lipids) also start to diffuse out of >> the box like they should, but in some a part of the molecule still jumps >> (as I could observe in xy direction), while the rest doesn't, leading to >> artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr >> file in the -s option, or a gro file (with only complete molecules), same >> result. >> >> >> I'd be glad if somebody could give me a hint. >> >> >> Cheers >> >> Sabine >> >> >> >> -- >> Dr. Sabine Reißer >> Theoretical Chemical Biology >> Institute of Physical Chemistry >> Karlsruhe Institute of Technology >> >> -- >> 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. >> > > > > -- > Best Regards, > Ganesh Shahane > -- > 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. > -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv -pbc nojump
On 9/2/15 7:17 AM, Reisser, Sabine (IPC) wrote: Thanks for the reply, but I don't want the lipids to jump from one edge of the box to the other, which they do with this option, even though they remain complete. Making molecules whole should be the first step, followed by removing jumps. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -Justin Cheers Sabine -- Dr. Sabine Reißer Theoretical Chemical Biology Institute of Physical Chemistry Karlsruhe Institute of Technology Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se im Auftrag von Ganesh Shahane Gesendet: Mittwoch, 2. September 2015 12:19 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] trjconv -pbc nojump Hi Reisser, Instead of using -pbc nojump, use -pbc whole. On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) < sabine.reis...@kit.edu> wrote: Hi, I want to use trjconv -pbc nojump to create a trajectory without box jumping of molecules. The molecules (lipids) also start to diffuse out of the box like they should, but in some a part of the molecule still jumps (as I could observe in xy direction), while the rest doesn't, leading to artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr file in the -s option, or a gro file (with only complete molecules), same result. I'd be glad if somebody could give me a hint. Cheers Sabine -- Dr. Sabine Reißer Theoretical Chemical Biology Institute of Physical Chemistry Karlsruhe Institute of Technology -- 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. -- Best Regards, Ganesh Shahane -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv -pbc nojump
Thanks for the reply, but I don't want the lipids to jump from one edge of the box to the other, which they do with this option, even though they remain complete. Cheers Sabine -- Dr. Sabine Reißer Theoretical Chemical Biology Institute of Physical Chemistry Karlsruhe Institute of Technology Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se im Auftrag von Ganesh Shahane Gesendet: Mittwoch, 2. September 2015 12:19 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] trjconv -pbc nojump Hi Reisser, Instead of using -pbc nojump, use -pbc whole. On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) < sabine.reis...@kit.edu> wrote: > Hi, > > > I want to use trjconv -pbc nojump to create a trajectory without box > jumping of molecules. The molecules (lipids) also start to diffuse out of > the box like they should, but in some a part of the molecule still jumps > (as I could observe in xy direction), while the rest doesn't, leading to > artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr > file in the -s option, or a gro file (with only complete molecules), same > result. > > > I'd be glad if somebody could give me a hint. > > > Cheers > > Sabine > > > > -- > Dr. Sabine Reißer > Theoretical Chemical Biology > Institute of Physical Chemistry > Karlsruhe Institute of Technology > > -- > 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. > -- Best Regards, Ganesh Shahane -- 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] trjconv -pbc nojump
Hi Reisser, Instead of using -pbc nojump, use -pbc whole. On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) < sabine.reis...@kit.edu> wrote: > Hi, > > > I want to use trjconv -pbc nojump to create a trajectory without box > jumping of molecules. The molecules (lipids) also start to diffuse out of > the box like they should, but in some a part of the molecule still jumps > (as I could observe in xy direction), while the rest doesn't, leading to > artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr > file in the -s option, or a gro file (with only complete molecules), same > result. > > > I'd be glad if somebody could give me a hint. > > > Cheers > > Sabine > > > > -- > Dr. Sabine Reißer > Theoretical Chemical Biology > Institute of Physical Chemistry > Karlsruhe Institute of Technology > > -- > 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. > -- Best Regards, Ganesh Shahane -- 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] trjconv -dt issue
Hi, On Thu, Aug 20, 2015 at 4:00 PM Matthias Ernst < matthias.er...@physik.uni-freiburg.de> wrote: > Thanks for your explanation, Mark. > > Concerning energy files and eneconv: > - I will try double-precision eneconv, as I don't mind larger files. > - In reply to the advice to "reset" the time of the energy files: how to > do it? I intended you to try eneconv -settime 0 for each file. > eneconv has no option for this, although the help states: > "With one file specified for -f: > Reads one energy file and writes another, applying the -dt, -offset, -t0 > and -settime options and converting to a different format if necessary > (indicated by file extentions)." > Strangely, the -t0 option does not exist in eneconv (GROMACS 4.6.5) and > if I try nevertheless, it states "Invalid command line argument: -t0". > Is that an error in the help or was the option just forgotten for the command line parsing of eneconv? > Looks like it :-( > - The eneconv -offset option seems to do nothing for me (or I looked at > the wrong spot). What does it do and how is supposed to work? > See doc string for -dt (so not useful for you) > - And last: eneconv has, in contrast to trjconv, no -skip option which > would allow for using every nth frame instead of choosing by time. Is > that intended? Right now, it could be helpful for me, so I would like to > state my request for it ;-) > Fair enough. My plan to fix such issues in the future is to move all energy writing to the TNG format introduced in 5.0, and now there is no need for two separate tools to do the same thing (and neither doing it very well). A further option for you is to use gmxdump to get the data in a text format - where the step number will be clear and potentially useful. That's a one-way trip, however - you won't get the data back into .edr format. There are some third-party MD analysis packages that might help, I have no idea. Concerning xtc files: > Obviously, the data types storing the step counter as well as the > timestamp are too small for my data. The step counter overflows quite > rapidly, I think we changed the step counter to a 64-bit integer before GROMACS 4.5. Doubtless some places print it badly, but I don't think you're doing 10^19 steps. > but also the time only works for ps steps up to 1.6777216E7 > (i.e. ~16.777mus). Going further, only even numbers are stored. This > gives a nasty number of "Timesteps at t=... don't match" messages when > using gmxcheck to see if everything went alright, obscuring real errors > that may be in between. > Yep. This gear is fast becoming out of date. > Is there any chance of saving the correct times in the trajectory file > (like using double-precision like for eneconv) or do I have to take care > of this separately? Or is there some other format I could use to save > the data efficiently? > Unless you run mdrun in double precision, the step number is the only reliable thing, unfortunately. Internally, the magnitude of the step number and time is only used for trivia, and clearly there are a number of things that could be improved about how we handle writing and post-processing data. Mark Thanks a lot, > Matthias > > > On 08/20/2015 12:56 PM, Mark Abraham wrote: > > Hi, > > > > This is indeed problematic. The .edr format (and its tools) are designed > > with limitations that were not really a problem 10 years ago. One of the > > limitations is that the time itself is stored in the same precision as > the > > simulation data, and this starts to lose precision as the simulation > > proceeds into the millions of MD steps. > > > > I think your practical course is to keep the simulation in the chunks > that > > you already have, and do your subsampling from them. You may get a better > > result if you pre-process each chunk to "start" from zero time (or making > > smaller chunks if you need to). This will help by keeping the side of the > > stride closer to the absolute value of the time. > > > > Another alternative is to pre-process the chunks with a double-precision > > eneconv, which will write the times in double precision. That won't help > if > > they're stored wrongly in the first place, but may help you handle some > > longer trajectory (at cost of more disk space). > > > > Mark > > > > On Wed, Aug 19, 2015 at 11:50 PM Matthias Ernst < > > matthias.er...@physik.uni-freiburg.de> wrote: > > > >> Hello, > >> > >> I have a quite long continuous trajectory coming from several initial > >> input pieces (cluster crashed...) that I want to downsample, as a start > >> from 0.5ps timestep in the source files to just 1ps and later bigger > >> timesteps. > >> > >> Using the -dt option of trjconv (GROMACS 4.6.5.), there seem to be > >> rounding issues which leads to times at .5ps being written from some > >> timestamp on (4.1943e+06). Is this a known behaviour? > >> > >> Related to this, what does the following sentence in the help for > >> trjconv -dt mean: > >> "This option relies on the accuracy of th
Re: [gmx-users] trjconv -dt issue
Thanks for your explanation, Mark. Concerning energy files and eneconv: - I will try double-precision eneconv, as I don't mind larger files. - In reply to the advice to "reset" the time of the energy files: how to do it? eneconv has no option for this, although the help states: "With one file specified for -f: Reads one energy file and writes another, applying the -dt, -offset, -t0 and -settime options and converting to a different format if necessary (indicated by file extentions)." Strangely, the -t0 option does not exist in eneconv (GROMACS 4.6.5) and if I try nevertheless, it states "Invalid command line argument: -t0". Is that an error in the help or was the option just forgotten for the command line parsing of eneconv? - The eneconv -offset option seems to do nothing for me (or I looked at the wrong spot). What does it do and how is supposed to work? - And last: eneconv has, in contrast to trjconv, no -skip option which would allow for using every nth frame instead of choosing by time. Is that intended? Right now, it could be helpful for me, so I would like to state my request for it ;-) Concerning xtc files: Obviously, the data types storing the step counter as well as the timestamp are too small for my data. The step counter overflows quite rapidly, but also the time only works for ps steps up to 1.6777216E7 (i.e. ~16.777mus). Going further, only even numbers are stored. This gives a nasty number of "Timesteps at t=... don't match" messages when using gmxcheck to see if everything went alright, obscuring real errors that may be in between. Is there any chance of saving the correct times in the trajectory file (like using double-precision like for eneconv) or do I have to take care of this separately? Or is there some other format I could use to save the data efficiently? Thanks a lot, Matthias On 08/20/2015 12:56 PM, Mark Abraham wrote: > Hi, > > This is indeed problematic. The .edr format (and its tools) are designed > with limitations that were not really a problem 10 years ago. One of the > limitations is that the time itself is stored in the same precision as the > simulation data, and this starts to lose precision as the simulation > proceeds into the millions of MD steps. > > I think your practical course is to keep the simulation in the chunks that > you already have, and do your subsampling from them. You may get a better > result if you pre-process each chunk to "start" from zero time (or making > smaller chunks if you need to). This will help by keeping the side of the > stride closer to the absolute value of the time. > > Another alternative is to pre-process the chunks with a double-precision > eneconv, which will write the times in double precision. That won't help if > they're stored wrongly in the first place, but may help you handle some > longer trajectory (at cost of more disk space). > > Mark > > On Wed, Aug 19, 2015 at 11:50 PM Matthias Ernst < > matthias.er...@physik.uni-freiburg.de> wrote: > >> Hello, >> >> I have a quite long continuous trajectory coming from several initial >> input pieces (cluster crashed...) that I want to downsample, as a start >> from 0.5ps timestep in the source files to just 1ps and later bigger >> timesteps. >> >> Using the -dt option of trjconv (GROMACS 4.6.5.), there seem to be >> rounding issues which leads to times at .5ps being written from some >> timestamp on (4.1943e+06). Is this a known behaviour? >> >> Related to this, what does the following sentence in the help for >> trjconv -dt mean: >> "This option relies on the accuracy of the times in your input >> trajectory, so if these are inaccurate use the -timestep option to >> modify the time (this can be done simultaneously)." >> How can I change the input timestep to get a "proper" output of output >> frames? I tried to use -timestep 1 it to my trajectory with 0.5ps >> timestep and it seems to produce "correct" timestamps in 1ps steps in >> the output file but the coordinates still are those of the initial >> frames with the 0.5ps timestamps, meaning it just relabels the >> timestamps of the frames. Using "-timestep 0.5 -dt 1" together does not >> change the result compared to "-dt 1" only. >> >> If I rather use the "-t0 0" option, I can "reset" the time of the first >> frame and then, it looks like it writes the "correct" 1ps stepped frames >> with 1ps timestamps, but starting at time 0. As I have several >> trajectory pieces from a continuous timeseries to concatenate, I would >> have to run trjconv once more just to correct and "reset" the time to >> its initial value, which means a lot of unnecessary data transfer, >> especially in the case of long trajectories. >> Is this really necessary or is there another way to get a "proper" >> downsampling? >> I know I can use the -skip 2 option but e.g. not for eneconv which only >> supports -dt and has the same issues. Further, just using -skip 2 is not >> possible if some input files are at 0.5ps, but some other already at 1ps >> tim
Re: [gmx-users] trjconv -dt issue
Hi, This is indeed problematic. The .edr format (and its tools) are designed with limitations that were not really a problem 10 years ago. One of the limitations is that the time itself is stored in the same precision as the simulation data, and this starts to lose precision as the simulation proceeds into the millions of MD steps. I think your practical course is to keep the simulation in the chunks that you already have, and do your subsampling from them. You may get a better result if you pre-process each chunk to "start" from zero time (or making smaller chunks if you need to). This will help by keeping the side of the stride closer to the absolute value of the time. Another alternative is to pre-process the chunks with a double-precision eneconv, which will write the times in double precision. That won't help if they're stored wrongly in the first place, but may help you handle some longer trajectory (at cost of more disk space). Mark On Wed, Aug 19, 2015 at 11:50 PM Matthias Ernst < matthias.er...@physik.uni-freiburg.de> wrote: > Hello, > > I have a quite long continuous trajectory coming from several initial > input pieces (cluster crashed...) that I want to downsample, as a start > from 0.5ps timestep in the source files to just 1ps and later bigger > timesteps. > > Using the -dt option of trjconv (GROMACS 4.6.5.), there seem to be > rounding issues which leads to times at .5ps being written from some > timestamp on (4.1943e+06). Is this a known behaviour? > > Related to this, what does the following sentence in the help for > trjconv -dt mean: > "This option relies on the accuracy of the times in your input > trajectory, so if these are inaccurate use the -timestep option to > modify the time (this can be done simultaneously)." > How can I change the input timestep to get a "proper" output of output > frames? I tried to use -timestep 1 it to my trajectory with 0.5ps > timestep and it seems to produce "correct" timestamps in 1ps steps in > the output file but the coordinates still are those of the initial > frames with the 0.5ps timestamps, meaning it just relabels the > timestamps of the frames. Using "-timestep 0.5 -dt 1" together does not > change the result compared to "-dt 1" only. > > If I rather use the "-t0 0" option, I can "reset" the time of the first > frame and then, it looks like it writes the "correct" 1ps stepped frames > with 1ps timestamps, but starting at time 0. As I have several > trajectory pieces from a continuous timeseries to concatenate, I would > have to run trjconv once more just to correct and "reset" the time to > its initial value, which means a lot of unnecessary data transfer, > especially in the case of long trajectories. > Is this really necessary or is there another way to get a "proper" > downsampling? > I know I can use the -skip 2 option but e.g. not for eneconv which only > supports -dt and has the same issues. Further, just using -skip 2 is not > possible if some input files are at 0.5ps, but some other already at 1ps > time steps. > > Thank you for your help, > Matthias > > -- > Progress... http://www.phdcomics.com/comics/archive.php?comicid=1611 > -- > 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] trjconv command not found
On 5/26/15 12:38 PM, Poncho Arvayo Zatarain wrote: Hello, when i use the command echo "0"|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 i have this: command not found: trjconv. What can i do? http://www.gromacs.org/Documentation/Installation_Instructions_5.0#getting-access-to-gromacs-after-installation If you're using the version 5.1 beta, there is no separate trjconv binary/link. Everything is in the gmx binary (gmx trjconv ...) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv: choosing name for a large number of output gro files
Hello, You can use the -sep flag with trjconv command ave your output files serially numbered from 0. Regards Abhishek On Wed, Apr 29, 2015 at 10:12 PM, Athina Meletiou wrote: > Dear Gromacs users, > > I want to use trjconv to extract frames from a long simulation in implicit > solvent. I am wondering though if there is a way to predefine the filenames > of the output .gro files. > > Let's say that I want to get 10 .gro files that would go by the names* > > 0.gro > 1.gro > 2.gro > 3.gro > 4.gro > 5.gro > 6.gro > 7.gro > 8.gro > 9.gro > 00010.gro > > *(in reality I want 1 frames each time, so 0.gro up to 0.gro) > > Is it possible to do it directly through Gromacs/trjconv? I will have > thousands of files to go through little by little, so I thought it would be > good if I could avoid having to rename them with a script afterwards, if > it's possible to directly name them through trjconv. > > Any help would be greatly appreciated :) > > Thank you very much in advance. > > > > > This message and any attachment are intended solely for the addressee > and may contain confidential information. If you have received this > message in error, please send it back to me, and immediately delete it. > > Please do not use, copy or disclose the information contained in this > message or in any attachment. Any views or opinions expressed by the > author of this email do not necessarily reflect the views of the > University of Nottingham. > > This message has been checked for viruses but the contents of an > attachment may still contain software viruses which could damage your > computer system, you are advised to perform your own checks. Email > communications with the University of Nottingham may be monitored as > permitted by UK legislation. > > -- > 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] trjconv for cutting the trajectory in small subtrajectories
Thanks my friendsI checked new trajectory by gmxcheck and get following text: Reading frame 0 time 7000.000 # Atoms 8383 Precision 0.001 (nm) Reading frame 5000 time 17000.000 Item #frames Timestep (ps) Step 5501 2 Time 5501 2 Lambda 0 Coords 5501 2 Velocities 0 Forces 0 Box 5501 2 Reading frame is 5000 but desired frames are 5500 frame. I'm confused.best On Saturday, April 25, 2015 5:42 PM, James Lord wrote: Hi Mahboobeh,I recommend checking the created trajectories with gmx check. CheersJames On Sun, Apr 26, 2015 at 12:39 AM, Ming Tang wrote: Hi,-e is end frame, -b is the start one. Sent from my Huawei Mobile Mahboobeh Eslami wrote: hi GMx user I simulated protein-ligand comolex with gromacs. total simulation time is 20ns. when I use trjconv for cutting the trajectory in small subtrajectories from 1ps to 17000ps by following command: trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000 I see following text in terminal window; Reading frame 0 time 1.000 Precision of md-nopbc.xtc is 0.001 (nm) Using output precision of 0.001 (nm) -> frame 3500 time 17000.000 -> frame 3000 time 16000.000 I think the generated trajectory is incomplete because saved frame is incomplete. please guide me. Many thanks tobest -- 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] trjconv for cutting the trajectory in small subtrajectories
On 4/25/15 9:24 AM, Mahboobeh Eslami wrote: Thanks my friends I checked new trajectory by gmxcheck and get following text: Reading frame 0 time 7000.000 # Atoms 8383 Precision 0.001 (nm) Reading frame5000 time 17000.000 Item#frames Timestep (ps) Step 55012 Time 55012 Lambda 0 Coords55012 Velocities 0 Forces 0 Box 55012 Reading frame is 5000 but desired frames are 5500 frame. I'm confused. best Again, this is irrelevant; it's a buffered progress indicator that has a fixed interval for printing (1000 past a certain point). You have 5501 frames (5500 + the first, inclusive, so 5501). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv for cutting the trajectory in small subtrajectories
Hi Mahboobeh, I recommend checking the created trajectories with gmx check. Cheers James On Sun, Apr 26, 2015 at 12:39 AM, Ming Tang wrote: > Hi,-e is end frame, -b is the start one. > > Sent from my Huawei Mobile > > Mahboobeh Eslami wrote: > > hi GMx user I simulated protein-ligand comolex with gromacs. total > simulation time is 20ns. when I use trjconv for cutting the trajectory > in small subtrajectories from 1ps to 17000ps by following command: > trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000 > I see following text in terminal window; > Reading frame 0 time 1.000 > Precision of md-nopbc.xtc is 0.001 (nm) > Using output precision of 0.001 (nm) > -> frame 3500 time 17000.000-> frame 3000 time 16000.000 > I think the generated trajectory is incomplete because saved frame is > incomplete. please guide me. > Many thanks tobest > -- > 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] trjconv for cutting the trajectory in small subtrajectories
On 4/25/15 7:52 AM, Mahboobeh Eslami wrote: hi GMx user I simulated protein-ligand comolex with gromacs. total simulation time is 20ns. when I use trjconv for cutting the trajectory in small subtrajectories from 1ps to 17000ps by following command: trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000 I see following text in terminal window; Reading frame 0 time 1.000 Precision of md-nopbc.xtc is 0.001 (nm) Using output precision of 0.001 (nm) -> frame 3500 time 17000.000-> frame 3000 time 16000.000 The output frame number doesn't necessarily reflect what's actually written; it's just a simple progress indicator. Use gmxcheck to verify the contents of the new trajectory. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv for cutting the trajectory in small subtrajectories
hi dear mingYes. Sorry, I've used the following command: trjconv -f md.xtc -s md.tpr -n index.ndx -b 1 -e 17000 but I do not get the desired result.best On Saturday, April 25, 2015 5:09 PM, Ming Tang wrote: #yiv1199526006 -- .yiv1199526006EmailQuote {margin-left:1pt;padding-left:4pt;border-left:#80 2px solid;}#yiv1199526006 Hi,-e is end frame, -b is the start one. Sent from my Huawei Mobile Mahboobeh Eslami wrote: hi GMx user I simulated protein-ligand comolex with gromacs. total simulation time is 20ns. when I use trjconv for cutting the trajectory in small subtrajectories from 1ps to 17000ps by following command: trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000 I see following text in terminal window; Reading frame 0 time 1.000 Precision of md-nopbc.xtc is 0.001 (nm) Using output precision of 0.001 (nm) -> frame 3500 time 17000.000 -> frame 3000 time 16000.000 I think the generated trajectory is incomplete because saved frame is incomplete. please guide me. Many thanks tobest -- 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] trjconv for cutting the trajectory in small subtrajectories
Hi,-e is end frame, -b is the start one. Sent from my Huawei Mobile Mahboobeh Eslami wrote: hi GMx user I simulated protein-ligand comolex with gromacs. total simulation time is 20ns. when I use trjconv for cutting the trajectory in small subtrajectories from 1ps to 17000ps by following command: trjconv -f md.xtc -s md.tpr -n index.ndx -e 1 -b 17000 I see following text in terminal window; Reading frame 0 time 1.000 Precision of md-nopbc.xtc is 0.001 (nm) Using output precision of 0.001 (nm) -> frame 3500 time 17000.000-> frame 3000 time 16000.000 I think the generated trajectory is incomplete because saved frame is incomplete. please guide me. Many thanks tobest -- 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] trjconv mismatch
Hi Jennifer, You can extract the first frame using the same logic and save it as PDB/GRO. Then you can use that structure as reference for the second pass. However, in this case it seems more logical to just write out a PDB trajectory directly and use 'cat' to combine them in a single file. Hope it helps, Tsjerk On Wed, Jan 14, 2015 at 10:07 AM, Jennifer Vo wrote: > Dear Mark, > Many thanks for your reply. > My command was: > > trjconv_mpi -f md-*.trr -n index.ndx -timestep 100 -o md-*-timestep100.xtc > > for every trr file, then concatenate by using > > trjcat_mpi -f md-*-timestep100.xtc -n index.ndx -o md-timestep100.xtc > > For index.ndx: > make_ndx_mpi -f md.gro -o index.ndx > and chose #1 for Protein. > > Many thanks for any help! > Regards, > Jennifer > > > On Wed, Jan 14, 2015 at 9:09 AM, Mark Abraham > wrote: > > > On Wed, Jan 14, 2015 at 9:00 AM, Jennifer Vo > wrote: > > > > > Dear All, > > > I have got this error while running trjconv from .xtc to .pdb file. The > > > System includes 8 Protein (4622 Atoms each, x8 = 36976 Atoms). 135978 > is > > > the total number of Atoms in the System. The index.ndx was created from > > > md.gro file, and I Chose #1 for Protein. I don't know where is the > > original > > > error of the mismatch here > > > Fatal error: > > > Index[4622] 135978 is larger than the number of atoms in the > > > trajectory file (36976). There is a mismatch in the contents > > > of your -f, -s and/or -n files. > > > > > > I would appreciate for any help. > > > > > > > Providing your actual command lines and interactive choices would help. > If > > you'd done the right things, you'd probably not be having a problem, so > > we'll need to know what things you actually did. ;-) > > > > Also, use gmx check on the .xtc and .tpr files, and less on the .ndx > files > > to see whether these files contain the things you think they do. > > > > Mark > > > > Jennifer. > > > -- > > > 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. > -- Tsjerk A. Wassenaar, Ph.D. -- 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] trjconv mismatch
Dear Mark, Many thanks for your reply. My command was: trjconv_mpi -f md-*.trr -n index.ndx -timestep 100 -o md-*-timestep100.xtc for every trr file, then concatenate by using trjcat_mpi -f md-*-timestep100.xtc -n index.ndx -o md-timestep100.xtc For index.ndx: make_ndx_mpi -f md.gro -o index.ndx and chose #1 for Protein. Many thanks for any help! Regards, Jennifer On Wed, Jan 14, 2015 at 9:09 AM, Mark Abraham wrote: > On Wed, Jan 14, 2015 at 9:00 AM, Jennifer Vo wrote: > > > Dear All, > > I have got this error while running trjconv from .xtc to .pdb file. The > > System includes 8 Protein (4622 Atoms each, x8 = 36976 Atoms). 135978 is > > the total number of Atoms in the System. The index.ndx was created from > > md.gro file, and I Chose #1 for Protein. I don't know where is the > original > > error of the mismatch here > > Fatal error: > > Index[4622] 135978 is larger than the number of atoms in the > > trajectory file (36976). There is a mismatch in the contents > > of your -f, -s and/or -n files. > > > > I would appreciate for any help. > > > > Providing your actual command lines and interactive choices would help. If > you'd done the right things, you'd probably not be having a problem, so > we'll need to know what things you actually did. ;-) > > Also, use gmx check on the .xtc and .tpr files, and less on the .ndx files > to see whether these files contain the things you think they do. > > Mark > > Jennifer. > > -- > > 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] trjconv mismatch
On Wed, Jan 14, 2015 at 9:00 AM, Jennifer Vo wrote: > Dear All, > I have got this error while running trjconv from .xtc to .pdb file. The > System includes 8 Protein (4622 Atoms each, x8 = 36976 Atoms). 135978 is > the total number of Atoms in the System. The index.ndx was created from > md.gro file, and I Chose #1 for Protein. I don't know where is the original > error of the mismatch here > Fatal error: > Index[4622] 135978 is larger than the number of atoms in the > trajectory file (36976). There is a mismatch in the contents > of your -f, -s and/or -n files. > > I would appreciate for any help. > Providing your actual command lines and interactive choices would help. If you'd done the right things, you'd probably not be having a problem, so we'll need to know what things you actually did. ;-) Also, use gmx check on the .xtc and .tpr files, and less on the .ndx files to see whether these files contain the things you think they do. Mark Jennifer. > -- > 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] trjconv mismatch in number of atoms
On 1/13/15 10:15 AM, Jennifer Vo wrote: Dear Experts, I am running a trjconv from xtc files to pdb file but have got this error: Fatal error: Index[4622] 135978 is larger than the number of atoms in the trajectory file (36976). There is a mismatch in the contents of your -f, -s and/or -n files. I don't know where the origin of the Problem, the index.ndx was created from md.gro file, the *.xtc (8 Proteins in a box, so I type #1 to have the index of 8 Proteins, each Protein has 4622 Atoms). The trajectory has 36976 Atoms which is 4622 * 8 and 135978 is the total number of Atoms in the This means you chose "Protein" as the only group saved in the .xtc (xtc-grps/compressed-x-grps). If you want to do analysis, you need to re-create your index file and perhaps make a matching .tpr file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv during transfer of .trr
Hello Johnny, Try gmxcheck -f file.trr - Eric On Sun, Dec 14, 2014 at 3:58 PM, Johnny Lu wrote: > > seems to be fine for slurm resource manager... so far. > > On Sun, Dec 14, 2014 at 5:50 PM, Johnny Lu wrote: > > > > Alternatively, is there a way to quickly check how many ns or frames do a > > .trr file contain? > > > > On Sun, Dec 14, 2014 at 5:47 PM, Johnny Lu > wrote: > >> > >> Hi. > >> > >> Before the queue manager of the cluster finishes transferring the .trr > >> file to my homedirectory, if I start trjconv, > >> and trjconv finishes running (which takes about half an hour) after the > >> .trr file (6 GB) completes transferring to my home directory, > >> > >> will the converted .trr contains as many ns as the original .trr? > >> > >> I used trjconv to only get rid of the water in the .trr file. > >> > >> > >> Or... part of the .trr file will get chop off when i convert with > trjconv? > >> > >> > >> Thank you for your help. > >> > > > -- > 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] trjconv during transfer of .trr
seems to be fine for slurm resource manager... so far. On Sun, Dec 14, 2014 at 5:50 PM, Johnny Lu wrote: > > Alternatively, is there a way to quickly check how many ns or frames do a > .trr file contain? > > On Sun, Dec 14, 2014 at 5:47 PM, Johnny Lu wrote: >> >> Hi. >> >> Before the queue manager of the cluster finishes transferring the .trr >> file to my homedirectory, if I start trjconv, >> and trjconv finishes running (which takes about half an hour) after the >> .trr file (6 GB) completes transferring to my home directory, >> >> will the converted .trr contains as many ns as the original .trr? >> >> I used trjconv to only get rid of the water in the .trr file. >> >> >> Or... part of the .trr file will get chop off when i convert with trjconv? >> >> >> Thank you for your help. >> > -- 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] trjconv during transfer of .trr
Alternatively, is there a way to quickly check how many ns or frames do a .trr file contain? On Sun, Dec 14, 2014 at 5:47 PM, Johnny Lu wrote: > > Hi. > > Before the queue manager of the cluster finishes transferring the .trr > file to my homedirectory, if I start trjconv, > and trjconv finishes running (which takes about half an hour) after the > .trr file (6 GB) completes transferring to my home directory, > > will the converted .trr contains as many ns as the original .trr? > > I used trjconv to only get rid of the water in the .trr file. > > > Or... part of the .trr file will get chop off when i convert with trjconv? > > > Thank you for your help. > -- 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] trjconv precision lost from double to single conversion
On Fri, Dec 12, 2014 at 4:31 PM, Johnny Lu wrote: > > Hi. I'm using gromacs 4.6.7 > > If the trr trajectory file is from double precision calculation, and I use > single precision trjconv to make a single precision trr trajectory, how > much precision will I lose in position and in force? > You'll go from practically infinite precision for any such quantity to about 6 significant figures, ie. double floating-point precision to single. Their representations are kind of like scientific notation. Read up on wikipedia about those :-) 1, 0.1, 0.01, or 0.001 angstrom and Newton? > That depends on the magnitude of the numbers. You're getting a change in relative precision. Is the lost of precision acceptable? > Depends what you're using them for. > I noticed that single precision trr seems to take about half the hard disk > space of double precision trr. > Yep. Mark > > Thank you. > -- > 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] trjconv precision lost from double to single conversion
nevermind the 2nd question. it does reduce to about 1/10 size. On Fri, Dec 12, 2014 at 10:41 AM, Johnny Lu wrote: > > When I test the disk space that I would save by getting rid the water in > the trajectory, I found that only make the trajectory 1/4 as large as the > original. > The trajectory has both position and force. > > Yet, the proteins only have about 1/10 the number of atoms of the whole > system. > > Group 0 ( System) has 29859 elements > Group 1 (Protein) has 2598 elements > > Should the trajectory file size reduced to 1/4 instead of 1/10? > > The command that I used was: > echo -e "1\n1\n" | $GMXHOME/trjconv_d -f $In_Traj -o $Out_Traj -s $In_ptr > -pbc mol -ur compact -center -force > > Thanks again. > > On Fri, Dec 12, 2014 at 10:31 AM, Johnny Lu > wrote: >> >> Hi. I'm using gromacs 4.6.7 >> >> If the trr trajectory file is from double precision calculation, and I >> use single precision trjconv to make a single precision trr trajectory, how >> much precision will I lose in position and in force? >> >> 1, 0.1, 0.01, or 0.001 angstrom and Newton? >> >> Is the lost of precision acceptable? >> >> I noticed that single precision trr seems to take about half the hard >> disk space of double precision trr. >> >> Thank you. >> > -- 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] trjconv precision lost from double to single conversion
When I test the disk space that I would save by getting rid the water in the trajectory, I found that only make the trajectory 1/4 as large as the original. The trajectory has both position and force. Yet, the proteins only have about 1/10 the number of atoms of the whole system. Group 0 ( System) has 29859 elements Group 1 (Protein) has 2598 elements Should the trajectory file size reduced to 1/4 instead of 1/10? The command that I used was: echo -e "1\n1\n" | $GMXHOME/trjconv_d -f $In_Traj -o $Out_Traj -s $In_ptr -pbc mol -ur compact -center -force Thanks again. On Fri, Dec 12, 2014 at 10:31 AM, Johnny Lu wrote: > > Hi. I'm using gromacs 4.6.7 > > If the trr trajectory file is from double precision calculation, and I use > single precision trjconv to make a single precision trr trajectory, how > much precision will I lose in position and in force? > > 1, 0.1, 0.01, or 0.001 angstrom and Newton? > > Is the lost of precision acceptable? > > I noticed that single precision trr seems to take about half the hard disk > space of double precision trr. > > Thank you. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjconv with or without water?
On 11/8/14 5:19 PM, Thomas Lipscomb wrote: Dear gmx-users, I am following the tutorial below but it doesn't mention choosing a group (see command line dump below, I have to choose between 0 and 5). I am trying to insert a small protein into a membrane so I think I should choose 0 or 5 depending on whether I should keep the water molecules. I mean maybe I should remove the water and choose 5 because I am inserting the protein into the membrane and the water molecules around the protein would get in the way? I want to simulate the membrane with water molecules around it, though. In this case, the choice of output is largely irrelevant. The subsequent construction steps will remove water either way. -Justin Thanks. Sincerely, Thomas "(2) Use trjconv to remove periodicity: gmx trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact" http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html [tlipscomb@prime-radiant KALP]$ /usr/local/gromacs/bin/gmx trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact GROMACS:gmx trjconv, VERSION 5.0.1 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit GroenhofChristoph Junghans Peter Kasson Carsten Kutzner Per LarssonJustin A. Lemkul Magnus LundborgPieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey ShvetsovMichael Shirts Alfons Sijbers Peter Tieleman Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2014, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx trjconv, VERSION 5.0.1 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact Will write gro: Coordinate file in Gromos-87 format Reading file em.tpr, VERSION 5.0.1 (single precision) Reading file em.tpr, VERSION 5.0.1 (single precision) Select group for output Group 0 ( System) has 17365 elements Group 1 ( Other) has 6400 elements Group 2 ( DPPC) has 6400 elements Group 3 ( Water) has 10965 elements Group 4 (SOL) has 10965 elements Group 5 ( non-Water) has 6400 elements -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv gets stuck on frame
Hi, Parallel file systems do give uneven service (e.g. one file has a chunk that lives somewhere that was under high load right when you asked for it...), so given that you can read the files normally on a normal filesystem, then you should double-check Stampede's user guides for how to make best use of their file systems, and/or take up the issue further with the admins there. Cheers, Mark On Mon, Oct 27, 2014 at 11:40 AM, Eric Smoll wrote: > Hi Mark, > > i understand. It wasn't getting stuck in one place, if I skip over the > problem time when executed from the beginning the slowdown still occurs. > > I am working on the Stampede Supercomputer using their install of gromacs > and for reasons I do not understand, this extremely slow processing only > occurs for some trajectories on Stampede. Thinking there was some problem > with the login nodes, I tried this on a compute node with the same results > - slow processing. > > I transferred my trajectory to my laptop, installed the same version of > gromacs, and processed it with trjconv at a reasonable speed. > > Best, > Eric > > > On Mon, Oct 27, 2014 at 5:33 AM, Mark Abraham > wrote: > > > On Sun, Oct 26, 2014 at 11:44 PM, Eric Smoll > wrote: > > > > > Hi Mark, > > > > > > Thank you for responding so rapidly. I should note that identical > > > processing (I use a script) on the trajectories produced by slightly > > > different chemical systems had no problem and trajconv produced a > > complete > > > processed trajectory. > > > > > > However, when processing the problematic few with trajconv, the > > trajectory > > > that is output is incomplete (the trjconv output has fewer frames than > > the > > > input trajectory). > > > > > > This is definitely not problem with the change in output frequency of > > > progress reports to the terminal. > > > > > > I am not sure if the -b flag is telling me anything. I move it around > and > > > it still seems to get stuck. I have ~30,000 atoms in my system. The > first > > > 120 ps are processed in ~ 5 seconds. The next 4 ps take ~ 30 sec. My > > > trajectory is many nanoseconds long. > > > > > > > The point is to try to see whether the issue happens x steps into the > > trajectory, or only at around t=120ps. Does it happen if you are using > -pbc > > somethingelse? Does it happen if you copy the file to some other > filesystem > > before using -pbc whole? One needs to find a pattern before one can guess > > where the problem might lie. > > > > > > > Again, my other chemically similar systems do no hang like this and the > > > simulation procedure is scripted so it is consistent across my > different > > > chemical systems. > > > > > > > OK. It's possible your simulation system is doing something pathological > in > > that trajectory, which somehow does not agree with the implementation of > > -pbc whole (I'm guessing wildly here), but one would need to try the > above > > kinds of experiments to probe that, and or visualize the trajectory in > some > > viewing program. > > > > Mark > > > > I am using gromacs/4.6.5. > > > > > > Best, > > > Eric > > > > > > On Sun, Oct 26, 2014 at 5:21 PM, Mark Abraham < > mark.j.abra...@gmail.com> > > > wrote: > > > > > > > Hi, > > > > > > > > The output does drop in frequency at some point, so that might be all > > you > > > > are seeing. Experiment with -b and values around the putative problem > > > area. > > > > > > > > Mark > > > > On Oct 26, 2014 6:59 PM, "Eric Smoll" wrote: > > > > > > > > > Hello Gromacs users, > > > > > > > > > > I have a trajectory file script18_o.trr that I am trying to > process. > > > > Using > > > > > gmxcheck, this file appears to be complete. When I execute the > > command > > > > > below > > > > > > > > > > trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr > > -o > > > > > tmp1.trr -pbc whole << EOF > > > > > 0 > > > > > EOF > > > > > > > > > > the code moves quickly through the first few hundred frames only to > > > > > consistently get stuck on frame 300... > > > > > > > > > > trn version: GMX_trn_file (single precision) > > > > > -> frame320 time 128.000-> frame300 time > 120.000 > > > > > > > > > > How do I troubleshoot the problem? > > > > > > > > > > -Eric > > > > > -- > > > > > 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 > > > >
Re: [gmx-users] trjconv gets stuck on frame
Hi Mark, i understand. It wasn't getting stuck in one place, if I skip over the problem time when executed from the beginning the slowdown still occurs. I am working on the Stampede Supercomputer using their install of gromacs and for reasons I do not understand, this extremely slow processing only occurs for some trajectories on Stampede. Thinking there was some problem with the login nodes, I tried this on a compute node with the same results - slow processing. I transferred my trajectory to my laptop, installed the same version of gromacs, and processed it with trjconv at a reasonable speed. Best, Eric On Mon, Oct 27, 2014 at 5:33 AM, Mark Abraham wrote: > On Sun, Oct 26, 2014 at 11:44 PM, Eric Smoll wrote: > > > Hi Mark, > > > > Thank you for responding so rapidly. I should note that identical > > processing (I use a script) on the trajectories produced by slightly > > different chemical systems had no problem and trajconv produced a > complete > > processed trajectory. > > > > However, when processing the problematic few with trajconv, the > trajectory > > that is output is incomplete (the trjconv output has fewer frames than > the > > input trajectory). > > > > This is definitely not problem with the change in output frequency of > > progress reports to the terminal. > > > > I am not sure if the -b flag is telling me anything. I move it around and > > it still seems to get stuck. I have ~30,000 atoms in my system. The first > > 120 ps are processed in ~ 5 seconds. The next 4 ps take ~ 30 sec. My > > trajectory is many nanoseconds long. > > > > The point is to try to see whether the issue happens x steps into the > trajectory, or only at around t=120ps. Does it happen if you are using -pbc > somethingelse? Does it happen if you copy the file to some other filesystem > before using -pbc whole? One needs to find a pattern before one can guess > where the problem might lie. > > > > Again, my other chemically similar systems do no hang like this and the > > simulation procedure is scripted so it is consistent across my different > > chemical systems. > > > > OK. It's possible your simulation system is doing something pathological in > that trajectory, which somehow does not agree with the implementation of > -pbc whole (I'm guessing wildly here), but one would need to try the above > kinds of experiments to probe that, and or visualize the trajectory in some > viewing program. > > Mark > > I am using gromacs/4.6.5. > > > > Best, > > Eric > > > > On Sun, Oct 26, 2014 at 5:21 PM, Mark Abraham > > wrote: > > > > > Hi, > > > > > > The output does drop in frequency at some point, so that might be all > you > > > are seeing. Experiment with -b and values around the putative problem > > area. > > > > > > Mark > > > On Oct 26, 2014 6:59 PM, "Eric Smoll" wrote: > > > > > > > Hello Gromacs users, > > > > > > > > I have a trajectory file script18_o.trr that I am trying to process. > > > Using > > > > gmxcheck, this file appears to be complete. When I execute the > command > > > > below > > > > > > > > trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr > -o > > > > tmp1.trr -pbc whole << EOF > > > > 0 > > > > EOF > > > > > > > > the code moves quickly through the first few hundred frames only to > > > > consistently get stuck on frame 300... > > > > > > > > trn version: GMX_trn_file (single precision) > > > > -> frame320 time 128.000-> frame300 time 120.000 > > > > > > > > How do I troubleshoot the problem? > > > > > > > > -Eric > > > > -- > > > > 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
Re: [gmx-users] trjconv gets stuck on frame
On Sun, Oct 26, 2014 at 11:44 PM, Eric Smoll wrote: > Hi Mark, > > Thank you for responding so rapidly. I should note that identical > processing (I use a script) on the trajectories produced by slightly > different chemical systems had no problem and trajconv produced a complete > processed trajectory. > > However, when processing the problematic few with trajconv, the trajectory > that is output is incomplete (the trjconv output has fewer frames than the > input trajectory). > > This is definitely not problem with the change in output frequency of > progress reports to the terminal. > > I am not sure if the -b flag is telling me anything. I move it around and > it still seems to get stuck. I have ~30,000 atoms in my system. The first > 120 ps are processed in ~ 5 seconds. The next 4 ps take ~ 30 sec. My > trajectory is many nanoseconds long. > The point is to try to see whether the issue happens x steps into the trajectory, or only at around t=120ps. Does it happen if you are using -pbc somethingelse? Does it happen if you copy the file to some other filesystem before using -pbc whole? One needs to find a pattern before one can guess where the problem might lie. > Again, my other chemically similar systems do no hang like this and the > simulation procedure is scripted so it is consistent across my different > chemical systems. > OK. It's possible your simulation system is doing something pathological in that trajectory, which somehow does not agree with the implementation of -pbc whole (I'm guessing wildly here), but one would need to try the above kinds of experiments to probe that, and or visualize the trajectory in some viewing program. Mark I am using gromacs/4.6.5. > > Best, > Eric > > On Sun, Oct 26, 2014 at 5:21 PM, Mark Abraham > wrote: > > > Hi, > > > > The output does drop in frequency at some point, so that might be all you > > are seeing. Experiment with -b and values around the putative problem > area. > > > > Mark > > On Oct 26, 2014 6:59 PM, "Eric Smoll" wrote: > > > > > Hello Gromacs users, > > > > > > I have a trajectory file script18_o.trr that I am trying to process. > > Using > > > gmxcheck, this file appears to be complete. When I execute the command > > > below > > > > > > trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr -o > > > tmp1.trr -pbc whole << EOF > > > 0 > > > EOF > > > > > > the code moves quickly through the first few hundred frames only to > > > consistently get stuck on frame 300... > > > > > > trn version: GMX_trn_file (single precision) > > > -> frame320 time 128.000-> frame300 time 120.000 > > > > > > How do I troubleshoot the problem? > > > > > > -Eric > > > -- > > > 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] trjconv gets stuck on frame
Hi Mark, Thank you for responding so rapidly. I should note that identical processing (I use a script) on the trajectories produced by slightly different chemical systems had no problem and trajconv produced a complete processed trajectory. However, when processing the problematic few with trajconv, the trajectory that is output is incomplete (the trjconv output has fewer frames than the input trajectory). This is definitely not problem with the change in output frequency of progress reports to the terminal. I am not sure if the -b flag is telling me anything. I move it around and it still seems to get stuck. I have ~30,000 atoms in my system. The first 120 ps are processed in ~ 5 seconds. The next 4 ps take ~ 30 sec. My trajectory is many nanoseconds long. Again, my other chemically similar systems do no hang like this and the simulation procedure is scripted so it is consistent across my different chemical systems. I am using gromacs/4.6.5. Best, Eric On Sun, Oct 26, 2014 at 5:21 PM, Mark Abraham wrote: > Hi, > > The output does drop in frequency at some point, so that might be all you > are seeing. Experiment with -b and values around the putative problem area. > > Mark > On Oct 26, 2014 6:59 PM, "Eric Smoll" wrote: > > > Hello Gromacs users, > > > > I have a trajectory file script18_o.trr that I am trying to process. > Using > > gmxcheck, this file appears to be complete. When I execute the command > > below > > > > trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr -o > > tmp1.trr -pbc whole << EOF > > 0 > > EOF > > > > the code moves quickly through the first few hundred frames only to > > consistently get stuck on frame 300... > > > > trn version: GMX_trn_file (single precision) > > -> frame320 time 128.000-> frame300 time 120.000 > > > > How do I troubleshoot the problem? > > > > -Eric > > -- > > 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] trjconv gets stuck on frame
Hi, The output does drop in frequency at some point, so that might be all you are seeing. Experiment with -b and values around the putative problem area. Mark On Oct 26, 2014 6:59 PM, "Eric Smoll" wrote: > Hello Gromacs users, > > I have a trajectory file script18_o.trr that I am trying to process. Using > gmxcheck, this file appears to be complete. When I execute the command > below > > trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr -o > tmp1.trr -pbc whole << EOF > 0 > EOF > > the code moves quickly through the first few hundred frames only to > consistently get stuck on frame 300... > > trn version: GMX_trn_file (single precision) > -> frame320 time 128.000-> frame300 time 120.000 > > How do I troubleshoot the problem? > > -Eric > -- > 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] trjconv pbc options
Hi Rinu, There's a suggested workflow on the Gromacs site. 'nojump' goes before 'center' because the centering may add a shift that messes up the jumps. 'whole' doean't actually change anything, so it can be used anytime before fitting, which messes up the PBC. Cheers, Tsjerk On Sep 19, 2014 6:26 AM, "RINU KHATTRI" wrote: > hello Tsjerk Wassenaar > can we use both command pbc whole and pbc nojump and in which stage of > simulation we have to use it because in the tutorial it is written > before center the protein in the box > thanks in advance > > On Thu, Sep 18, 2014 at 9:40 PM, Tsjerk Wassenaar > wrote: > > Hi Prathiba, > > > > With -pbc nojump, an atom that jumps from one side to the box to the > other > > is reset, so the trajectory is made continuous. If the molecule is broken > > and you remove jumps, the molecule will stay broken. > > > > With -pbc whole, the molecule is made whole, which means that the atoms > are > > shifted such that all bonds have the correct lengths. The algorithm > starts > > with the first atom of the molecule, so if that atom jumps over PBC, then > > -pbc whole will make the whole molecule jump. > > > > Cheers, > > > > Tsjerk > > > > On Thu, Sep 18, 2014 at 5:54 PM, Justin Lemkul wrote: > > > >> > >> > >> On 9/18/14 11:51 AM, pratibha kapoor wrote: > >> > >>> Hi users > >>> > >>> I have question regarding difference between pbc whole and pbc nojump > >>> options using trjconv. Please help me understand this. > >>> > >>> > >> Have you read trjconv -h yet? > >> > >> -Justin > >> > >> -- > >> == > >> > >> Justin A. Lemkul, Ph.D. > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow > >> > >> Department of Pharmaceutical Sciences > >> School of Pharmacy > >> Health Sciences Facility II, Room 601 > >> University of Maryland, Baltimore > >> 20 Penn St. > >> Baltimore, MD 21201 > >> > >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > >> http://mackerell.umaryland.edu/~jalemkul > >> > >> == > >> > >> -- > >> 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. > >> > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > -- > > 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] trjconv pbc options
hello Tsjerk Wassenaar can we use both command pbc whole and pbc nojump and in which stage of simulation we have to use it because in the tutorial it is written before center the protein in the box thanks in advance On Thu, Sep 18, 2014 at 9:40 PM, Tsjerk Wassenaar wrote: > Hi Prathiba, > > With -pbc nojump, an atom that jumps from one side to the box to the other > is reset, so the trajectory is made continuous. If the molecule is broken > and you remove jumps, the molecule will stay broken. > > With -pbc whole, the molecule is made whole, which means that the atoms are > shifted such that all bonds have the correct lengths. The algorithm starts > with the first atom of the molecule, so if that atom jumps over PBC, then > -pbc whole will make the whole molecule jump. > > Cheers, > > Tsjerk > > On Thu, Sep 18, 2014 at 5:54 PM, Justin Lemkul wrote: > >> >> >> On 9/18/14 11:51 AM, pratibha kapoor wrote: >> >>> Hi users >>> >>> I have question regarding difference between pbc whole and pbc nojump >>> options using trjconv. Please help me understand this. >>> >>> >> Have you read trjconv -h yet? >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 601 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> == >> >> -- >> 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. >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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] trjconv pbc options
Hi Prathiba, With -pbc nojump, an atom that jumps from one side to the box to the other is reset, so the trajectory is made continuous. If the molecule is broken and you remove jumps, the molecule will stay broken. With -pbc whole, the molecule is made whole, which means that the atoms are shifted such that all bonds have the correct lengths. The algorithm starts with the first atom of the molecule, so if that atom jumps over PBC, then -pbc whole will make the whole molecule jump. Cheers, Tsjerk On Thu, Sep 18, 2014 at 5:54 PM, Justin Lemkul wrote: > > > On 9/18/14 11:51 AM, pratibha kapoor wrote: > >> Hi users >> >> I have question regarding difference between pbc whole and pbc nojump >> options using trjconv. Please help me understand this. >> >> > Have you read trjconv -h yet? > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > > -- > 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. > -- Tsjerk A. Wassenaar, Ph.D. -- 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] trjconv pbc options
On 9/18/14 11:51 AM, pratibha kapoor wrote: Hi users I have question regarding difference between pbc whole and pbc nojump options using trjconv. Please help me understand this. Have you read trjconv -h yet? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] trjconv -s
That all depends on what kind of analysis you are trying to do. Many functions that require a '-s' structure flag also accept PDB files as structure files, so you should be able to get by with just your PDB file. If any of the programs give you an issue, it's probably a result of a difference in naming convention between gromacs libraries and the CHARMM FF that you use. On Tue, Sep 16, 2014 at 10:28 AM, xy21hb wrote: > > > > Thanks for all the help. however, is there any way I can generate a .tpr > file so that I can use my traj in gromacs for further analysis? > > > Best, > > > Yao > > > > > > > > > > > At 2014-09-16 11:13:03, "Samuel Bowerman" wrote: > >Yao, > > > >There is a tool that comes with VMD called "catdcd". You can call it from > >the command line and convert it with minimal effort. See here: > >http://www.ks.uiuc.edu/Development/MDTools/catdcd/ > > > >Take care, > >Sam Bowerman > > > >On Tue, Sep 16, 2014 at 9:05 AM, xy21hb wrote: > > > >> Dear all, > >> > >> > >> I have a .dcd trajectory with .psf from NAMD and would like to convert > the > >> trajectory to > >> > >> GMX format .gro or .trr by using trjconv. > >> > >> > >> Would it be possible to do this without generating .tpr? > >> If not, I wonder what other possible ways would be. > >> Thanks, > >> > >> > >> Yao > >> > >> > >> > >> > >> > >> At 2014-09-16 09:59:45, "Mark Abraham" > wrote: > >> >On Tue, Sep 16, 2014 at 3:51 PM, xy21hb wrote: > >> > > >> >> Dear all, > >> >> > >> >> > >> >> .tpr in trjconv is supposed to be optional, but it is in fact > required. > >> >> Any thoughts about that? > >> >> > >> > > >> >Ahem "in fact required for what I am trying to do" ;-) trjconv will > insist > >> >on a .tpr file if you ask it to do something that needs information it > can > >> >only get there. But since you haven't told us your trjconv command, or > any > >> >detail below, then we can't really help. > >> > > >> >Mark > >> > > >> >I have a .dcd trajectory and .psf from NAMD and would like to convert > to > >> >> GMX format. > >> >> > >> >> > >> >> Thanks, > >> >> > >> >> > >> >> Yao > >> >> -- > >> >> 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. > -- 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] trjconv -s
Yao, There is a tool that comes with VMD called "catdcd". You can call it from the command line and convert it with minimal effort. See here: http://www.ks.uiuc.edu/Development/MDTools/catdcd/ Take care, Sam Bowerman On Tue, Sep 16, 2014 at 9:05 AM, xy21hb wrote: > Dear all, > > > I have a .dcd trajectory with .psf from NAMD and would like to convert the > trajectory to > > GMX format .gro or .trr by using trjconv. > > > Would it be possible to do this without generating .tpr? > If not, I wonder what other possible ways would be. > Thanks, > > > Yao > > > > > > At 2014-09-16 09:59:45, "Mark Abraham" wrote: > >On Tue, Sep 16, 2014 at 3:51 PM, xy21hb wrote: > > > >> Dear all, > >> > >> > >> .tpr in trjconv is supposed to be optional, but it is in fact required. > >> Any thoughts about that? > >> > > > >Ahem "in fact required for what I am trying to do" ;-) trjconv will insist > >on a .tpr file if you ask it to do something that needs information it can > >only get there. But since you haven't told us your trjconv command, or any > >detail below, then we can't really help. > > > >Mark > > > >I have a .dcd trajectory and .psf from NAMD and would like to convert to > >> GMX format. > >> > >> > >> Thanks, > >> > >> > >> Yao > >> -- > >> 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] trjconv -s
On Tue, Sep 16, 2014 at 7:35 PM, xy21hb wrote: > Dear all, > > > I have a .dcd trajectory with .psf from NAMD and would like to convert the > trajectory to > > GMX format .gro or .trr by using trjconv. > > > Would it be possible to do this without generating .tpr? > If not, I wonder what other possible ways would be. > VMD can do it, I suppose. > Thanks, > > > Yao > > > > > > At 2014-09-16 09:59:45, "Mark Abraham" wrote: > >On Tue, Sep 16, 2014 at 3:51 PM, xy21hb wrote: > > > >> Dear all, > >> > >> > >> .tpr in trjconv is supposed to be optional, but it is in fact required. > >> Any thoughts about that? > >> > > > >Ahem "in fact required for what I am trying to do" ;-) trjconv will insist > >on a .tpr file if you ask it to do something that needs information it can > >only get there. But since you haven't told us your trjconv command, or any > >detail below, then we can't really help. > > > >Mark > > > >I have a .dcd trajectory and .psf from NAMD and would like to convert to > >> GMX format. > >> > >> > >> Thanks, > >> > >> > >> Yao > >> -- > >> 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. > -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India *"All work and no play makes Jack a dull boy...”* -- 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] trjconv -s
On Tue, Sep 16, 2014 at 3:51 PM, xy21hb wrote: > Dear all, > > > .tpr in trjconv is supposed to be optional, but it is in fact required. > Any thoughts about that? > Ahem "in fact required for what I am trying to do" ;-) trjconv will insist on a .tpr file if you ask it to do something that needs information it can only get there. But since you haven't told us your trjconv command, or any detail below, then we can't really help. Mark I have a .dcd trajectory and .psf from NAMD and would like to convert to > GMX format. > > > Thanks, > > > Yao > -- > 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] trjconv error
Thanks Justin , I'll continue by keeping all atoms in the next step. *--RK* On Thu, Nov 21, 2013 at 7:21 PM, Justin Lemkul wrote: > On Thu, Nov 21, 2013 at 8:17 PM, Rama Krishna Koppisetti < > ramkishn...@gmail.com> wrote: > > > Hi Justin, > > > > the groups that I selected in first invocation was: > > > > Group22 ( Water) has 28857 elements > > Group23 (SOL) has 28857 elements > > Group24 ( non-Water) has 8271 elements > > Group25 ( Water_and_ions) has 28870 elements > > Select a group: 24 > > Selected 24: 'non-Water' > > trn version: GMX_trn_file (single precision) > > Last frame 1500 time 15000.000-> frame 1500 time 15000.000 > > > > then for second command I selected the same group > > > > Group22 ( Water) has 28857 elements > > Group23 (SOL) has 28857 elements > > Group24 ( non-Water) has 8271 elements > > Group25 ( Water_and_ions) has 28870 elements > > Select a group: 24 > > Selected 24: 'non-Water' > > trn version: GMX_trn_file (single precision) > > Reading frame 0 time0.000 > > Setting output precision to 0.001 (nm) > > > > --- > > Program g_trjconv, VERSION 4.5.5 > > Source code file: > > /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c, line: 1166 > > > > Fatal error: > > Index[8263] 37121 is larger than the number of atoms in the > > trajectory file (8271). There is a mismatch in the contents > > of your -f, -s and/or -n files. > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > > > > Right, so there are more atoms in the .tpr file than the .trr, hence the > mismatch when trying to read in a .trr frame - it doesn't match the .tpr. > Rule of thumb - keep all the atoms until the very last step unless you want > to do more work creating different .tpr files. > > -Justin > > -- > > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > == > -- > 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] trjconv error
On Thu, Nov 21, 2013 at 8:17 PM, Rama Krishna Koppisetti < ramkishn...@gmail.com> wrote: > Hi Justin, > > the groups that I selected in first invocation was: > > Group22 ( Water) has 28857 elements > Group23 (SOL) has 28857 elements > Group24 ( non-Water) has 8271 elements > Group25 ( Water_and_ions) has 28870 elements > Select a group: 24 > Selected 24: 'non-Water' > trn version: GMX_trn_file (single precision) > Last frame 1500 time 15000.000-> frame 1500 time 15000.000 > > then for second command I selected the same group > > Group22 ( Water) has 28857 elements > Group23 (SOL) has 28857 elements > Group24 ( non-Water) has 8271 elements > Group25 ( Water_and_ions) has 28870 elements > Select a group: 24 > Selected 24: 'non-Water' > trn version: GMX_trn_file (single precision) > Reading frame 0 time0.000 > Setting output precision to 0.001 (nm) > > --- > Program g_trjconv, VERSION 4.5.5 > Source code file: > /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c, line: 1166 > > Fatal error: > Index[8263] 37121 is larger than the number of atoms in the > trajectory file (8271). There is a mismatch in the contents > of your -f, -s and/or -n files. > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > Right, so there are more atoms in the .tpr file than the .trr, hence the mismatch when trying to read in a .trr frame - it doesn't match the .tpr. Rule of thumb - keep all the atoms until the very last step unless you want to do more work creating different .tpr files. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] trjconv error
Hi Justin, the groups that I selected in first invocation was: Group22 ( Water) has 28857 elements Group23 (SOL) has 28857 elements Group24 ( non-Water) has 8271 elements Group25 ( Water_and_ions) has 28870 elements Select a group: 24 Selected 24: 'non-Water' trn version: GMX_trn_file (single precision) Last frame 1500 time 15000.000-> frame 1500 time 15000.000 then for second command I selected the same group Group22 ( Water) has 28857 elements Group23 (SOL) has 28857 elements Group24 ( non-Water) has 8271 elements Group25 ( Water_and_ions) has 28870 elements Select a group: 24 Selected 24: 'non-Water' trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Setting output precision to 0.001 (nm) --- Program g_trjconv, VERSION 4.5.5 Source code file: /builddir/build/BUILD/gromacs-4.5.5/src/tools/gmx_trjconv.c, line: 1166 Fatal error: Index[8263] 37121 is larger than the number of atoms in the trajectory file (8271). There is a mismatch in the contents of your -f, -s and/or -n files. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors thanks On Thu, Nov 21, 2013 at 4:55 PM, Justin Lemkul wrote: > On Thu, Nov 21, 2013 at 5:50 PM, Rama wrote: > > > Hi > > > > After MD run, lipids are broken at the boundaries. I'm trying to fix > > trajectory by following command > > > > trjconv -f a.trr -o a1.trr -s b.tpr -pbc mol > > > > then I use a1.trr file(output file from above command) to make snapshots > by > > following command: > > > > trjconv -s b.tpr -f a1.trr -o c.gro -skip 5 -sep > > > > it shows some fatal error: > > Fatal error: > > Index[8271] 8272 is larger than the number of atoms in the > > trajectory file (8271). There is a mismatch in the contents > > of your -f, -s and/or -n files. > > > > > You haven't shown what group you are choosing for output in the first > invocation of trjconv, but it is fairly clear that you are not saving all > the necessary coordinates. > > -Justin > > -- > > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > == > -- > 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] trjconv error
On Thu, Nov 21, 2013 at 5:50 PM, Rama wrote: > Hi > > After MD run, lipids are broken at the boundaries. I'm trying to fix > trajectory by following command > > trjconv -f a.trr -o a1.trr -s b.tpr -pbc mol > > then I use a1.trr file(output file from above command) to make snapshots by > following command: > > trjconv -s b.tpr -f a1.trr -o c.gro -skip 5 -sep > > it shows some fatal error: > Fatal error: > Index[8271] 8272 is larger than the number of atoms in the > trajectory file (8271). There is a mismatch in the contents > of your -f, -s and/or -n files. > > You haven't shown what group you are choosing for output in the first invocation of trjconv, but it is fairly clear that you are not saving all the necessary coordinates. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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.