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
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
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
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
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 in .
make[2
]: Nothing to be done for `all-am'.
make[1]: Nothing to be done for `all-am'.
nom27267d:gromacs-4.0.7-mbh emily$
On Wed, May 12, 2010 at 10:10 AM, Emily Curtis
emilymariecur...@gmail.comwrote:
Here are all of the messages I get when I type make. I have been trying
to figure this out based on mailing
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]: ***
if that was why it
didn't work. Thank you for any help.
Emily
On Sat, May 8, 2010 at 5:13 AM, lina zhao0...@ntu.edu.sg wrote:
On 7/05/2010 11:59 PM, Emily Curtis wrote:
Hi Lina,
Did you ever figure out why you were getting the message:
gromacs checking size of void*... 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
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
Justin,
Thank you again! Your suggestion worked.
Emily
On Thu, May 6, 2010 at 11:55 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Emily Curtis wrote:
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 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
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
To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] Mac OS X with MKL
Emily Curtis wrote:
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
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