[gmx-users] compile template.c

Dear GMX users, I am trying to compile templete.c in template directory of gromacs-.4.5.3. However, when I type "make", I got the following errors with termination of compiling: gcc -L/home/h1y//lib -L/home/h1y/fftw3s/lib -o template template.o -lmd -lgmx -lfftw3f -lxml2 -lnsl -lm /

[gmx-users] turn-off Lennard-Jone interaction for a particular pair.

Dear GMX-users, I would like to turn off only the Lennerd-Jones interaction for a particular pair of atoms, while maintaining the electrostatic interaction. For example, the system consist of A, B, and C atoms. All of them have charge. I would like to turn off the Lennard-Jones self-interaction

[gmx-users] anisotripic polarization in water model

Dear GMX users, I am using GMX 4.5.3 I wnat to implement the anisotropic polarization of water, i.e. the polarizability is different in each direction. Is is possible with GROMACS? Can anybody help me how to do it? Thank you in advanced for all your helps/comments. Best, Jae H. Park ==

RE: [gmx-users] more than 100% CPU

but by checking the ns.day you > will see that the benefit is between 5% and 16% > > Chris. > > It means you are running a lot of parallel processes, but that does not > translate into a linear increase in speed.  So faster, but not 16X. > > Warren Gallin > > On 2011-08-18,

RE: [gmx-users] more than 100% CPU

] more than 100% CPU I believe that the current version of GROMACS supports threading, which does not require mpi. So mdrun is running threads at 100% of the activity of each of your 16 nodes, hence 1600%. Warren Gallin On 2011-08-18, at 5:19 PM, Park, Jae Hyun nmn wrote: > Hi GMX us

[gmx-users] GROMACS with GPU

Dear GMX users, I am installing GMX 4.5.3 with GPU. But, the CUDA in my GPU machine is ver 4.0. Can I use this version of CUDA and openmm-3.1.1? Or, do I have to re-install CUDA 3.2 and openmm-2.0 as described in manual? Thank you in advance for your kind instruction. Jae H. Park

[gmx-users] more than 100% CPU

Hi GMX users, I installed GMX 4.5.3 recently. But, when I just execute mdrun (without mpi, I did not installed mpi-version of mdrun), the use of CPU appears more than 100% ("top" command in LINUX). How is it possible? For example, I am using 16-node machine. And if I simply run "mdrun", then us

[gmx-users] compile template.c

Dear GMX users, Now, I am trying to write my own gromacs analysis code with gromacs 4.5.3. As a first test, when I run "make" in the directory of "template" I got the following message: -- cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -fun

[gmx-users] compile template.c

Dear GMX users, Now, I am trying to write my own gromacs analysis code with gromacs 4.5.3. As a first test, when I run "make" in the directory of "template" I got the following message: -- cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -fun

[gmx-users] make ghost atom

Dear all, I would like to change a specific atom into a ghost particle (no interaction with system) after some time (for example, 1ns). Is there any way to implement it in GROMACS? If I need change the code, what file do I have to look at? I would deeply appreciate any comments. Jae H. Park Jae