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.
[gmx-users] trjconv ndec not working
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.
[gmx-users] trjconv ndec not working
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.
