Re: [gmx-users] Simulations on GPU
Hi, I get this error when I try to run mdrun-gpu with a forcefield that has GROMOS interaction types: Fatal error: OpenMM does not support (some) of the provided interaction type(s) (G96Angle). Maybe it's possible to run a short simulation on a small system and not encounter the missing interactions? I don't know enough about how the forcefields work to know whether that would get past the error. -Keith I doesn't matter whether the simulation is short or the system small. You can exclude certain interaction types from the FF but then you'll end up with a most likely meaningless model. Rossen Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulations on GPU
OpenMM works with AMBER force-field. Then, to use OpenMM you have to change the force-field Il 13/01/2011 21:42, Keith Callenberg ha scritto: On Tue, Jan 4, 2011 at 3:17 PM, Rossen Apostolovros...@kth.se wrote: On 1/4/11 3:16 PM, Francesco Oteri wrote: Maybe the used force-field is wrong. mdrun-gpu is able to use the AMBER forcefield, but it is not possible using gromos force-field. When gromos force-field is used, the output is full of NaN Is that the case? mdrun should complain and exit if the FF isn't supported. I get this error when I try to run mdrun-gpu with a forcefield that has GROMOS interaction types: Fatal error: OpenMM does not support (some) of the provided interaction type(s) (G96Angle). Maybe it's possible to run a short simulation on a small system and not encounter the missing interactions? I don't know enough about how the forcefields work to know whether that would get past the error. -Keith Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_analyze with multiple sets
Hello, I have several files containing two columns, x and y (x is the same for all of them). I would like to calculate the average and standar deviation (as the error bar) for the y column for all my data sets. I have tried using g_analyze: g_analyze -n 3 -av average.xvg -errbar stddev -f set1.xvg set2.xvg set3.xvg I get several errors: set2.xvg: Command not found set3.xvg: Command not found And also: Set 2 is horter (0) than the previous set (1775) I have seen a similar error in the gromacs list archive, and the problem seemed to be the space before the . I remove this whitespace and also the space after the , but I get the same results. How could I solve this problem? Thanks a lot for your help in advance. Best wishes, Rebeca Garcia Postdoctoral student Santiago de Compostela University Spain rega...@hotmail.com
Re: [gmx-users] g_analyze with multiple sets
Rebeca García Fandiño wrote: Hello, I have several files containing two columns, x and y (x is the same for all of them). I would like to calculate the average and standar deviation (as the error bar) for the y column for all my data sets. I have tried using g_analyze: g_analyze -n 3 -av average.xvg -errbar stddev -f set1.xvg set2.xvg set3.xvg I get several errors: set2.xvg: Command not found set3.xvg: Command not found And also: Set 2 is horter (0) than the previous set (1775) I have seen a similar error in the gromacs list archive, and the problem seemed to be the space before the . I remove this whitespace and also the space after the , but I get the same results. How could I solve this problem? g_analyze does not take multiple simultaneous input. The referred to in the help text refers to data sets within the same .xvg file that are separated by . -Justin Thanks a lot for your help in advance. Best wishes, Rebeca Garcia Postdoctoral student Santiago de Compostela University Spain rega...@hotmail.com # # # # -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulations on GPU
On Fri, Jan 14, 2011 at 3:58 AM, Rossen Apostolov ros...@kth.se wrote: Hi, I get this error when I try to run mdrun-gpu with a forcefield that has GROMOS interaction types: Fatal error: OpenMM does not support (some) of the provided interaction type(s) (G96Angle). Maybe it's possible to run a short simulation on a small system and not encounter the missing interactions? I don't know enough about how the forcefields work to know whether that would get past the error. -Keith I doesn't matter whether the simulation is short or the system small. You can exclude certain interaction types from the FF but then you'll end up with a most likely meaningless model. Rossen Thank you, but I think you missed the point of my question. I was only trying to understand why Francesco might get output that is full of NaN instead of an error. -Keith Rossen -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] g_analyze with multiple sets
Thanks a lot for the clarification, now it works perfectly. Sorry for the confusion! Best wishes, Rebeca. Date: Fri, 14 Jan 2011 13:46:26 -0500 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] g_analyze with multiple sets Rebeca García Fandiño wrote: Hello, I have several files containing two columns, x and y (x is the same for all of them). I would like to calculate the average and standar deviation (as the error bar) for the y column for all my data sets. I have tried using g_analyze: g_analyze -n 3 -av average.xvg -errbar stddev -f set1.xvg set2.xvg set3.xvg I get several errors: set2.xvg: Command not found set3.xvg: Command not found And also: Set 2 is horter (0) than the previous set (1775) I have seen a similar error in the gromacs list archive, and the problem seemed to be the space before the . I remove this whitespace and also the space after the , but I get the same results. How could I solve this problem? g_analyze does not take multiple simultaneous input. The referred to in the help text refers to data sets within the same .xvg file that are separated by . -Justin Thanks a lot for your help in advance. Best wishes, Rebeca Garcia Postdoctoral student Santiago de Compostela University Spain rega...@hotmail.com # # # # -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
