[gmx-users] res_com in g_rdf

Hi. I am running simulations with DPPC and water molecules. I made groups from a set of atoms from each DPPC molecule (example: Group 1 = C1, C2, C3 Group 2 = C4, C5, C6). I want to calculate the rdf for the center of mass of each group from each DPPC molecule while excluding groups located o

Re: [gmx-users] g_rdf between bonded and nonbonded groups

Hi Justin, Thank you for your help. I will edit the topology file. I am running GROMACS 4.0.7. I can download the latest version. The command line I was using was: g_rdf -n index -rdf res_com -s full -surf -o rdf08SEPT10.xvg Emily On Wed, Sep 8, 2010 at 5:31 PM, Emily Curtis wrote: >

[gmx-users] g_rdf between bonded and nonbonded groups

I would like to calculate the inter- and intra-molecular radial distribution functions separately. I have read through g_rdf -h many times and I have a few questions: 1. I think that I may have to modify a trp file (and not use it for the simulations) by setting the nrexcl to the number of bonds

[gmx-users] luck works but demo fails

I think that I finally managed to get gromacs installed correctly. When I type luck in the command line I get a random phrase. When I try to run "demo" I get the following error messages: dyld: Library not loaded: libmkl_intel_lp64.dylib Referenced from: /Users/emily/gromacsfolder/bin/pdb2gmx

Re: [gmx-users] Help, Errors while compiling gromacs under Mac OS X 10.5 Leopard

e for `all-am'. Making all in images make[3]: Nothing to be done for `all'. Making all in online make[3]: Nothing to be done for `all'. make[2]: Nothing to be done for `all-am'. Making all in man Making all in man1 make[2]: Nothing to be done for `all'. make[2]: Nothing to be

Re: [gmx-users] Help, Errors while compiling gromacs under Mac OS X 10.5 Leopard

Here are all of the messages I get when I type "make". I have been trying to figure this out based on mailing list emails but I cant seem to find what I need to fix. Thank you for your help. Emily-Curtis-MacBook-Pro:gromacs-4.0.7-mbh emily$ make Making all in include Making all i

[gmx-users] Help, Errors while compiling gromacs under Mac OS X 10.5 Leopard

Dr. Bonner, I am trying to install gromacs on a mac. I am running Leopard. I can configure successfully, however, when I type "make" I am getting the same errors that you reported: make[5]: *** [nb_kernel010_ppc_altivec.lo] Error 1 make[4]: *** [all-recursive] Error 1 make[3]: *** [all-recurs

Re: [gmx-users] Re: configure error

that was why it didn't work. Thank you for any help. Emily On Sat, May 8, 2010 at 5:13 AM, lina wrote: > > On 7/05/2010 11:59 PM, Emily Curtis wrote: > > > Hi Lina, > > > > > > Did you ever figure out why you were getting the message: > > > >

[gmx-users] configure error

Hi Lina, Did you ever figure out why you were getting the message: gromacs checking size of void*... configure: error: cannot compute sizeof (void*) I am also getting this error. I have read the configure.log a million times and I still can't figure out why I am getting this message. The stran

Re: [gmx-users] luck message and running tests

Justin, Thank you again! Your suggestion worked. Emily On Thu, May 6, 2010 at 11:55 AM, Justin A. Lemkul wrote: > > > Emily Curtis wrote: > >> I was able to "make install". >> *After typing ./luck * >> >> I got the following message: I was

[gmx-users] luck message and running tests

I was able to "make install". *After typing ./luck * I got the following message: I was detained, I was restrained *Is that bad? Also, I am trying to run the tests and I keep getting:* ERROR: Can not find grompp in your path. Please source GMXRC and try again. Does anyone know how to fix thi

Re: [gmx-users] Mac OS X with MKL

is help. If you gat confused google for > gromacs intel. > > > > Best regards > > > > Anthony > > > > -Original Message- > > From: Justin A. Lemkul > > Sent: Wednesday, May 05, 2010 5:15 PM > > To: Discussion list for GROMACS users

[gmx-users] Mac OS X with MKL

Hi. I am also trying to build Gromacs with MKL on a Mac OS X. I get the same error that you reported: checking for mkl.h... yes checking for DftiComputeForward in -lmkl... no configure: error: Cannot find Intel Math Kernel Library >= 6.0 Did you ever figure out how to fix this? I would reall

[gmx-users] question about installing gromacs on a mac

I apologize in advance if this is a very stupid question. I am trying to configure GROMACS on a mac. I have the intel MKL installed. *When I type the following:* ./configure --with-fft=mkl CPPFLAGS="-I/Developer/opt/intel/Compiler/11.1/067/Frameworks/mkl/include" LDFLAGS="-L/Developer/opt/intel