RE: [gmx-users] Black whole simluations

Dear Ben, This is not really related to your question but I don't think gromacs can deal with such black hole simulations as the simulations implemented in gromacs are of classical mechanics. There is a group working on black hole modeling. They've also developed a problem environment calle

Re: [gmx-users] Black whole simluations

Ben If you have this dream, go for it. I'm pretty sure nobody did a gromacs simulation with Black holes yet and that really looks like a breakthrough in science as we know it Wish you the best of all luck ever Matheus On Fri, Mar 14, 2008 at 11:57 AM, roger han <[EMAIL PROTECTED]> wrote: > >

Re: [gmx-users] *.itp files

Quoting Sagittarius <[EMAIL PROTECTED]>: > Dear Gromacs users, > > I try to use Gromacs at the step: > pdb2gmx -f C:\Soft\Gromacs\Input\formaldehyde.pdb -o outputName.gro -p > outputName.top > pdb2gmx -f C:\Soft\Gromacs\Input\cyanide.pdb -o outputName.gro -p > outputName.top > How can I get fo

[gmx-users] *.itp files

Dear Gromacs users, I try to use Gromacs at the step: pdb2gmx -f C:\Soft\Gromacs\Input\formaldehyde.pdb -o outputName.gro -p outputName.top pdb2gmx -f C:\Soft\Gromacs\Input\cyanide.pdb -o outputName.gro -p outputName.top How can I get formaldehyde.itp and cyanide.itp if I have formaldehyde.pd

Re: e: [gmx-users] ambconv again

Alan <[EMAIL PROTECTED]> wrote: Hi Bruce, many thanks for your archive. Incidentally, I do use Mac! and I have quitted trying to adjust Makefile for ambconv to compile on Mac tiger intel. Although your ambconv compiles here, it is still not working (giving "Bus error"). But then you mentione

RE: [gmx-users] SGI installation problem

Hi David, I did as following and still getting the same error: % make -f scripts/Makefile There are some minor differences (apart from those related to the specifications and paths in my system) between the file that you sent me and the one in the script directory. May be the way that I try

Re: [gmx-users] SGI installation problem

Siavoush Dastmalchi wrote: Hi, As I mentioned before, the installation stopped with the error shown below. Looking for your kind attentions. Cheers, Siavoush Making all in contrib Making all in admin Making all in scripts make: file 'Makefile' line 417: syntax error *** Error code 1 (bu21)

RE: [gmx-users] SGI installation problem

Hi, As I mentioned before, the installation stopped with the error shown below. Looking for your kind attentions. Cheers, Siavoush Making all in contrib Making all in admin Making all in scripts make: file 'Makefile' line 417: syntax error *** Error code 1 (bu21) __

Re: [gmx-users] SGI installation problem - make_edi

Erik Lindahl wrote: Hi, One option would simply be to remove make_edi from Makefile.am. Unfortunately this tool has proven to be a bit buggy in the compile stage, and you won't need it for any normal simulations. The other fix would be to create separate static variables to use in the list

RE: [gmx-users] SGI installation problem

Hi, I did the following changes and it seems that problem has been fixed. But, then again I got the error saying that: syntax error in makefile line xxx ( I can't remember the exact error message now). Here is the changes on the make_edi file: { evStepOptions[evLINFIX], FALSE, etSTR, {&evParams

e: [gmx-users] ambconv again

Hi Bruce, many thanks for your archive. Incidentally, I do use Mac! and I have quitted trying to adjust Makefile for ambconv to compile on Mac tiger intel. Although your ambconv compiles here, it is still not working (giving "Bus error"). But then you mentioned you did "topolbuild". So I fetched

Re: [gmx-users] SGI installation problem

Hi, One option would simply be to remove make_edi from Makefile.am. Unfortunately this tool has proven to be a bit buggy in the compile stage, and you won't need it for any normal simulations. The other fix would be to create separate static variables to use in the list for reading option

RE: [gmx-users] SGI installation problem

Hi there, Now I am getting the following error. I can see that others had this problem before and there are couple of solutions in the archive suggested by the list. I was wondering which one should I consider. Some suggestions apparently didn't work, but others , I am not sure. Many thanks, Sia

[gmx-users] Postdoc/staff scientist opportunities: Gromacs & free energy

Hi, We've recently landed two major grants focused on membrane proteins/ ion channels and pushing new types of parallelization and free energy calculation algorithms in Gromacs. The projects will be quite flexible, but some of the important things we want to address are mixed shared-memory

Re: [gmx-users] SGI installation problem

Siavoush Dastmalchi wrote: Hi, Thanks to David for his suggestion. Now I have the following error. It is a bit of shame that I am hassling you, but I want GMX to work on my sgi. Cheers, Siavoush Here is the error message: gmx_spatial.c -Wp,-MDupdate,.deps/gmx_spatial.TPlo -o gmx_sp