Re: [gmx-users] trjconv_d errors
On Wed, Apr 8, 2015 at 7:50 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: Thats what I thought. About what? You've top-posted a reply to an email that had three different topics... there's nobody here paid to read minds ;-) I recieved no response, but can jimmy rigg the entire thing to be processed on 4.6.7 from a 5.0.1 run, however it looses the temperature? Again wildly unlikely, because no trajectory file stores the temperature, but since you won't describe what you're doing, you're likely to keep having to solve your problems on your own :-) Mark Sincerely, STephan L. Watkins, PhD *Gesendet:* Montag, 06. April 2015 um 02:51 Uhr *Von:* lloyd riggs lloyd.ri...@gmx.ch *An:* gmx-us...@gromacs.org *Betreff:* Re: [gmx-users] trjconv_d errors Dear All, I recentlly installed gromacs 5.0.1 and a few months later 5.0.4 (hoping there was adifference) as I am using terra grid with a 5.0.1 install. Now, I noticed 2 things, trjconv_d no matter what I do can not read or convert the .trr file, even with simple -f in.trr -o out.trr or .xtc files. I was simply interested mostly as my secound problem is, if I include anything other than the standard energy groups of protein non_protein (say x y z), the performance goes from 20 ns a day for my system, to 10 ns a day. Thus I was going to rerun everything after the grid usage with -rerun and a changed energy group list just to make my life easier. I checked all of this with 4.5.6, 4.6.7 versions and the trjconv_d -f in.trr -o out.trr or out.xtc works fine. It will even process a standard 5.0.1 in.trr file, however if I then try any type of rerun (as expected) I get a version error. Is this a) a bug and b) a if so or not, does someone have a work around? I have also tried gmx_d trjconv, and I searched the mail archives, and the only thing anyone mentioned was a 64 bit, vs a 32 bit Linux install delema, stating if the files were larger than a few gigs, there was a memory error. I origionally thought this the error, however decided to run test first with small 100MB-2 G runs to test it, and this was not the problem. Sincerely, Stephan L. Watkins, PhD -- 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_d errors
Thats what I thought. I recieved no response, but can jimmy rigg the entire thing to be processed on 4.6.7 from a 5.0.1 run, however it looses the temperature? Sincerely, STephan L. Watkins, PhD Gesendet:Montag, 06. April 2015 um 02:51 Uhr Von:lloyd riggs lloyd.ri...@gmx.ch An:gmx-us...@gromacs.org Betreff:Re: [gmx-users] trjconv_d errors Dear All, I recentlly installed gromacs 5.0.1 and a few months later 5.0.4 (hoping there was adifference) as I am using terra grid with a 5.0.1 install. Now, I noticed 2 things, trjconv_d no matter what I do can not read or convert the .trr file, even with simple -f in.trr -o out.trr or .xtc files. I was simply interested mostly as my secound problem is, if I include anything other than the standard energy groups of protein non_protein (say x y z), the performance goes from 20 ns a day for my system, to 10 ns a day. Thus I was going to rerun everything after the grid usage with -rerun and a changed energy group list just to make my life easier. I checked all of this with 4.5.6, 4.6.7 versions and the trjconv_d -f in.trr -o out.trr or out.xtc works fine. It will even process a standard 5.0.1 in.trr file, however if I then try any type of rerun (as expected) I get a version error. Is this a) a bug and b) a if so or not, does someone have a work around? I have also tried gmx_d trjconv, and I searched the mail archives, and the only thing anyone mentioned was a 64 bit, vs a 32 bit Linux install delema, stating if the files were larger than a few gigs, there was a memory error. I origionally thought this the error, however decided to run test first with small 100MB-2 G runs to test it, and this was not the problem. Sincerely, Stephan L. Watkins, PhD -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Cant 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_d errors
On Mon, Apr 6, 2015 at 2:51 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: Dear All, I recentlly installed gromacs 5.0.1 and a few months later 5.0.4 (hoping there was adifference) as I am using terra grid with a 5.0.1 install. We write release notes so that you can know what you're doing, rather than hope... Now, I noticed 2 things, trjconv_d no matter what I do can not read or convert the .trr file, even with simple -f in.trr -o out.trr or .xtc files. You're doing something wrong, but without a detailed description of input commands and output, nobody can help. cannot read and cannot convert are two completely different things, and look different on your terminal. Use gmx check on the trajectory files to be sure they contain what you think they do. I was simply interested mostly as my secound problem is, if I include anything other than the standard energy groups of protein non_protein (say x y z), the performance goes from 20 ns a day for my system, to 10 ns a day. Thus I was going to rerun everything after the grid usage with -rerun and a changed energy group list just to make my life easier. Wildly unlikely. You are surely varying something else as well. The general policy of doing reruns afterwards is an efficient one, however. I checked all of this with 4.5.6, 4.6.7 versions and the trjconv_d -f in.trr -o out.trr or out.xtc works fine. It will even process a standard 5.0.1 in.trr file, however if I then try any type of rerun (as expected) I get a version error. *what* version error? from what command? there's no version number in a .trr file, so you can't get a version error from doing a rerun on a .trr. Is this a) a bug and b) a if so or not, does someone have a work around? Can't tell, you haven't been precise enough, I'm afraid. Mark I have also tried gmx_d trjconv, and I searched the mail archives, and the only thing anyone mentioned was a 64 bit, vs a 32 bit Linux install delema, stating if the files were larger than a few gigs, there was a memory error. I origionally thought this the error, however decided to run test first with small 100MB-2 G runs to test it, and this was not the problem. Sincerely, Stephan L. Watkins, PhD -- 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_d errors
Dear All, I recentlly installed gromacs 5.0.1 and a few months later 5.0.4 (hoping there was adifference) as I am using terra grid with a 5.0.1 install. Now, I noticed 2 things, trjconv_d no matter what I do can not read or convert the .trr file, even with simple -f in.trr -o out.trr or .xtc files. I was simply interested mostly as my secound problem is, if I include anything other than the standard energy groups of protein non_protein (say x y z), the performance goes from 20 ns a day for my system, to 10 ns a day. Thus I was going to rerun everything after the grid usage with -rerun and a changed energy group list just to make my life easier. I checked all of this with 4.5.6, 4.6.7 versions and the trjconv_d -f in.trr -o out.trr or out.xtc works fine. It will even process a standard 5.0.1 in.trr file, however if I then try any type of rerun (as expected) I get a version error. Is this a) a bug and b) a if so or not, does someone have a work around? I have also tried gmx_d trjconv, and I searched the mail archives, and the only thing anyone mentioned was a 64 bit, vs a 32 bit Linux install delema, stating if the files were larger than a few gigs, there was a memory error. I origionally thought this the error, however decided to run test first with small 100MB-2 G runs to test it, and this was not the problem. Sincerely, Stephan L. Watkins, PhD -- 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.
