Re: [gmx-users] Simulations on GPU

2011-01-14 Thread Keith Callenberg
On Fri, Jan 14, 2011 at 3:58 AM, Rossen Apostolov 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 t

Re: [gmx-users] Simulations on GPU

2011-01-14 Thread Francesco Oteri
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 Apostolov wrote: On 1/4/11 3:16 PM, Francesco Oteri wrote: Maybe the used force-field is wrong. mdrun-gpu is a

Re: [gmx-users] Simulations on GPU

2011-01-14 Thread Rossen Apostolov
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 interac

Re: [gmx-users] Simulations on GPU

2011-01-13 Thread Keith Callenberg
On Tue, Jan 4, 2011 at 3:17 PM, Rossen Apostolov 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 ful

Re: [gmx-users] Simulations on GPU

2011-01-04 Thread Rossen Apostolov
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

Re: [gmx-users] Simulations on GPU

2011-01-04 Thread Francesco Oteri
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 Il 12/10/2010 03:00, Igor Leontyev ha scritto: Now I am able to run simulations on GPU but the output i

[gmx-users] Simulations on GPU

2010-10-11 Thread Igor Leontyev
Now I am able to run simulations on GPU but the output is weird. For example, temperature drops down to 270K while ref_t=298 (Tcoupl=andersen). Moreover, after several hours of simulations mdrun-gpu starts to output "NAN" energies and hangs up. Pre-run and post-run GPU memory test is always pas

[gmx-users] Simulations on GPU

2010-10-08 Thread Igor Leontyev
Finally, I compiled and ran simulations with gpu version of gromacs-4.5.1. There were several issues: 1) Precompiled OpenMM2.0 libraries and headers must be downloaded (which requires registration on their web page) and installed, otherwise cmake doesn't find some source files. 2) cmake sh

Re: [gmx-users] Simulations on GPU

2010-10-07 Thread Rossen Apostolov
Hi, On 10/6/10 3:48 AM, Igor Leontyev wrote: Szilárd wrote: The beta versions are all outdated, could you please use the latest source distribution (4.5.1) instead (or git from the release-4-5-patches branch)? The result is the same for both the distribution 4.5.1 and git from the release-

Re: [gmx-users] Simulations on GPU

2010-10-06 Thread Szilárd Páll
Dear Igor, Your output look _very_ weird, it seems as if CMake internal variable(s) were not initialized, which I have no clue how could have happened - the build generator works just fine for me. The only thing I can think of is that maybe your CMakeCache is corrupted. Could you please rerun cma

[gmx-users] Simulations on GPU

2010-10-05 Thread Igor Leontyev
Szilárd wrote: The beta versions are all outdated, could you please use the latest source distribution (4.5.1) instead (or git from the release-4-5-patches branch)? The result is the same for both the distribution 4.5.1 and git from the release-4-5-patches. See the output bellow.