Re: [gmx-users] Replica Exchange Error

Will do thanks. Ilya On Sun, Apr 12, 2009 at 7:50 PM, Mark Abraham wrote: > Joe Joe wrote: > >> It works just fine without RE. >> > > OK well that sounds like after a replica exchange attempt, some data > structure isn't being (re-)constructed correctly. See if you can construct a > pair of .tpr

Re: [gmx-users] Replica Exchange Error

Joe Joe wrote: It works just fine without RE. OK well that sounds like after a replica exchange attempt, some data structure isn't being (re-)constructed correctly. See if you can construct a pair of .tpr files that reproduce the problem with replica exchange after a small number of replica

Re: [gmx-users] Replica Exchange Error

It works just fine without RE. On Sat, Apr 11, 2009 at 8:49 PM, Mark Abraham wrote: > Joe Joe wrote: > >> Hi Justin, >> >> Thanks for helping me with this. >> On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Joe Joe wrote: >> >>How do I determine

Re: [gmx-users] Replica Exchange Error

Joe Joe wrote: Hi Justin, Thanks for helping me with this. On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul > wrote: Joe Joe wrote: How do I determine what those values should be? How does it affect the simulation? The header of your log

Re: [gmx-users] Replica Exchange Error

On Sat, Apr 11, 2009 at 8:13 PM, Justin A. Lemkul wrote: > > > Joe Joe wrote: > >> Hi Justin, >> >> Thanks for helping me with this. >> On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Joe Joe wrote: >> >>How do I determine what those values shou

Re: [gmx-users] Replica Exchange Error

Joe Joe wrote: Hi Justin, Thanks for helping me with this. On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul > wrote: Joe Joe wrote: How do I determine what those values should be? How does it affect the simulation? The header of your lo

Re: [gmx-users] Replica Exchange Error

On Sat, Apr 11, 2009 at 10:52 PM, Joe Joe wrote: > Hi Justin, > Thanks for helping me with this. > > On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul wrote: >> >> >> Joe Joe wrote: >>> >>> How do I determine what those values should be? How does it affect the >>> simulation? >>> >> >> The header

Re: [gmx-users] Replica Exchange Error

Hi Justin, Thanks for helping me with this. On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul wrote: > > > Joe Joe wrote: > >> How do I determine what those values should be? How does it affect the >> simulation? >> >> > The header of your log file should have printed what the initial guesses >

Re: [gmx-users] Replica Exchange Error

Joe Joe wrote: How do I determine what those values should be? How does it affect the simulation? The header of your log file should have printed what the initial guesses were. The -dd option sets how many PP nodes there are in the domain decomposition; using 4 cores, there are probably 3

Re: [gmx-users] Replica Exchange Error

How do I determine what those values should be? How does it affect the simulation? thanks, Ilya On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul wrote: > > > Joe Joe wrote: > >> Hi All, >> >> I get the following error when running replica exchange. I have 32 >> replica's with each replica runn

Re: [gmx-users] Replica Exchange Error

Joe Joe wrote: Hi All, I get the following error when running replica exchange. I have 32 replica's with each replica running on 4 processors (128 total). How do I decrease the domain decomposition cell size, -dss? What should I set it to? You're getting some hints from mdrun, I'd start