[gmx-users] Using the XTC library

2011-05-06 Thread Ryan S Davis (rsdavis1)
I am trying to use the XTC library in my code but I am just not good at this stuff. http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library I installed using ./configure --prefix=/$HOME/apps/xdrfile make install everything seemed to go well and the make check said everything passed.

[gmx-users] RE: gmx-users Digest, Vol 85, Issue 53

2011-05-08 Thread Ryan S Davis (rsdavis1)
ut it. But, I guess it still isnt seeing the library. Also, I tried compiling after appending the LIBDIR to my LD_LIBRARY_PATH and LD_RUN_PATH, neither worked. Message: 1 Date: Fri, 6 May 2011 22:31:23 -0500 From: "Ryan S Davis (rsdavis1)" Subject: [gmx-users] Using t

[gmx-users] Indexing problem when using genconf

2011-05-30 Thread Ryan S Davis (rsdavis1)
I wanted to copy a bilayer into a grid of 2x2x1 replicas. I used genconf and everything seemed to work fine exept that annoying feature that the command does not reorder the molecule types, so I end up with a .top file looking like this... 1 #include "martini_v2.1.itp" 2 #include "martini_v2

[gmx-users] Re: Indexing problem when using genconf

2011-06-03 Thread Ryan S Davis (rsdavis1)
Justin A. Lemkul wrote: > > > Ryan S Davis (rsdavis1) wrote: >> I wanted to copy a bilayer into a grid of 2x2x1 replicas. I used >> genconf and everything seemed to work fine exept that annoying feature >> that the command does not reorder the molecule types, so I

[gmx-users] mpi installation problems

2010-07-28 Thread Ryan S Davis (rsdavis1)
I am trying to install gromacs with MPI enabled on a cluster but it seems like fftw is giving me trouble. First, I compile everything without MPI just fine. FFTW is already on the cluster. I export pertinent variables... export CPPFLAGS=-I/opt/fftw/3.2.1/include export LDFLAGS=-L/opt/fftw/3.2.