Re: [gmx-users] Compile Gromacs for Blue Gene/L

Have a digg in the mailing list. I remember that someone has once shared... On 4/4/2007 6:15 AM, Mike Hanby wrote: Howdy, We are bringing a one rack (1024 node) IBM Blue Gene/L system online. I've been tasked with compiling Gromacs for the Blue Gene. We have the XL compilers installed (bl

[gmx-users] pairs types for decoupling

All, I'm using the CVS version of 3.3.1 from last week, and am trying to get the new pairs types Berk Hess has implemented to work for doing decoupling. There's an old e-mail here on the subject, which is all I've got to go by: http://www.gromacs.org/pipermail/gmx-developers/2006-March/001530.htm

[gmx-users] Compile Gromacs for Blue Gene/L

Howdy, We are bringing a one rack (1024 node) IBM Blue Gene/L system online. I've been tasked with compiling Gromacs for the Blue Gene. We have the XL compilers installed (blrts_xlc / mpixlc, etc), so I'll be using those rather than GNU. Has anyone on here successfully cross compiled Gromac

[gmx-users] request for patch and test program from 'Speeding up Parallel GROMACS'

Hi I was happy to see the 'Speeding up Parallel GROMACS' paper. I'd like to try the GROMACS patch for better all-to-all, as well as the all-to-all test program referred to on the paper. I can't find it on the GROMACS site. We've got a Cisco 6500 and when I run tcpdump during MPI runs I see a h

Re: [gmx-users] re: g_rms v. g_rmsdist

Hi Gleb, Apparently I wasn't clear enough. g_rmsdist calculates the average distance for each pair of atoms over time and then calculates, for each frame, the deviations from the average distance for each pair of atoms. Per frame, these deviations are summed and the square root is taken. You're r

[gmx-users] re: g_rms v. g_rmsdist

Hi Tsjerk, Thanks very much for the response. Just to make sure I understand correctly, g_rmsdist calculates an average interatom distance value for the reference structure. At a time t, a similar average interatom distance is calculated and the observed deviation is the difference between this

[gmx-users] background charge

I have a question about simulating metal ions in aqueous solution at an infinite diluition: say I have a metal ion (such as Ca2+ or Mg2+) and about a thousand water molecules. I have to compensate the non zero charge of the system with negative ions? As I can understand the use of a reaction field

Re: [gmx-users] ordered all-to-all patch

I have found it. Thanks for your patience, I don't know how I missed it. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Plea

Re: [gmx-users] ordered all-to-all patch

Chris Neale wrote: Thanks for the reply. Are you sure that it is there? I checked that prior to sending the fist request and I checked it again now. Ordered by date, the most recent entry is "StressCPU, version 2.0 09.02.2007" and next is "g_spatial 21.12.2006". In any event, I cleared my cache

Re: [gmx-users] Missing LJ interaction

David van der Spoel wrote: Steve Fiedler wrote: Thank you for looking over the input and for suggestions Mark. Unfortunately, a comparison of the topologies with diff revealed no inconsistencies. GROMACS can correctly recognize the presence of the significant repulsion (e+10) between atoms 1

Re: [gmx-users] ordered all-to-all patch

On Tue, Apr 03, 2007 at 10:16:12AM -0400, Chris Neale wrote: > Thanks for the reply. Are you sure that it is there? I checked that > prior to sending the fist request and I checked it again now. Ordered by > date, the most recent entry is "StressCPU, version 2.0 09.02.2007" and > next is "g_spat

Re: [gmx-users] ordered all-to-all patch

Thanks for the reply. Are you sure that it is there? I checked that prior to sending the fist request and I checked it again now. Ordered by date, the most recent entry is "StressCPU, version 2.0 09.02.2007" and next is "g_spatial 21.12.2006". In any event, I cleared my cache, used the reload b

Re: [gmx-users] ordered all-to-all patch

Hi Chris, the patch can be downloaded from the gromacs website: download -> user contributions -> contributed software -> gmx_alltoall Carsten [EMAIL PROTECTED] wrote: This is a fantastic development. I had wondered why my scaling was so much better for openmpi than for lam. Has the patch be

Re: [gmx-users] compare simulations between wt and mutate protein

Hi, Hi Andrea, I think it's a good thing to start another simulation by mutating the [EMAIL PROTECTED] Besides, it would be good to mutate the [EMAIL PROTECTED] back, to see if it goes the other way. In any case, you'll have to perform multiple simulations. For a strategy on comparing simulat