[gmx-users] g_dipoles questions

Dear All, I have few questions about g_dipoles, which are not explained in the manual (these questions are probably mostly to developers): 1) What method is used to calculate the epsilon? Is there a reference which can be cited? 2) I can't figure out the purpose of the option -enx. When I supply

Re: [gmx-users] Bug in g_energy for calculating heat capacity?

Zhang Zhigang wrote: Hi, all, Actually I think others have also noticed this bug: g_energy often generate incorrect heat capacity. When I checked the source code of gmx_energy.c, I found the calculation of heat capacity is only related with the fluctuation of temperature, which is

[gmx-users] Parallel run on a Quad Core

Thanks to all for helping me previously. Now i am unable to arrange the .tpr file for position restraint mdrun on a quad core as in version 4.0.2 grompp -np is not a valid comand can anybody help me in building a tpr file for parallel run on 4 cores of a quad core machine .I have installed gromacs

Re: [gmx-users] Parallel run on a Quad Core

Chitrita Dutta Roy wrote: Thanks to all for helping me previously. Now i am unable to arrange the .tpr file for position restraint mdrun on a quad core as in version 4.0.2 grompp -np is not a valid comand can anybody help me in building a tpr file for parallel run on 4 cores of a quad core

Re: [gmx-users] Parallel run on a Quad Core

But i can visually see that only one of my cores is running to 100% but i want 4 of them to work simultaneously giving me a guranteed 6-8 Gflops whereas right now i am just getting 2 .How can i achieve that...??? On Sun, Dec 21, 2008 at 6:05 PM, Justin A. Lemkul jalem...@vt.edu wrote:

Re: [gmx-users] Parallel run on a Quad Core

On Sun, Dec 21, 2008 at 5:04 PM, Chitrita Dutta Roy chitrita...@gmail.comwrote: Thanks to all for helping me previously. Now i am unable to arrange the .tpr file for position restraint mdrun on a quad core as in version 4.0.2 grompp -np is not a valid comand can anybody help me in building a

Re: [gmx-users] Parallel run on a Quad Core

Chitrita Dutta Roy wrote: Thanks to all for helping me previously. Now i am unable to arrange the .tpr file for position restraint mdrun on a quad core as in version 4.0.2 grompp -np is not a valid comand can anybody help me in building a tpr file for parallel run on 4 cores of a quad core

Re: [gmx-users] Parallel run on a Quad Core

I tried that way it basically creates 4 jobs and takes hold of 4 cpus but the problem is that it shows to take more time than it would normally without mpirun..and not only that a weird thing starts happening.Once being progressed to some steps it retreats back again to an older one and sometimes

Re: [gmx-users] Parallel run on a Quad Core

Chitrita Dutta Roy wrote: I tried that way it basically creates 4 jobs and takes hold of 4 cpus but the problem is that it shows to take more time than it would normally without mpirun..and not only that a weird thing starts happening.Once being progressed to some steps it retreats back

Re: [gmx-users] Parallel run on a Quad Core

tar -zxvf openmpi-1.2.8.tar.bz2 cd openmpi-1.2.8 ./configure make make install i had my fftw library installed. untarred gromacs went to its directory.. ./configure --enable-mpi --program_suffix=_mpi make make install grompp -f pr2.mdp -c em.gro -r em.gro -p scr8.top -n em.ndx -o pr.tpr mpirun

Re: [gmx-users] Parallel run on a Quad Core

Sorry for the first step i used manual extraction as that was a bzip package. On Sun, Dec 21, 2008 at 10:05 PM, Chitrita Dutta Roy chitrita...@gmail.comwrote: tar -zxvf openmpi-1.2.8.tar.bz2 cd openmpi-1.2.8 ./configure make make install i had my fftw library installed. untarred gromacs

Re: [gmx-users] Parallel run on a Quad Core

Chitrita Dutta Roy wrote: tar -zxvf openmpi-1.2.8.tar.bz2 cd openmpi-1.2.8 ./configure make make install i had my fftw library installed. untarred gromacs went to its directory.. ./configure --enable-mpi --program_suffix=_mpi make make install grompp -f pr2.mdp -c em.gro -r em.gro -p

Re: [gmx-users] Parallel run on a Quad Core

Thanks for your help. ok i have gone through that and even the wiki dirty install.Ok i will go through those once more and will see if it works.Thanks once again. On Sun, Dec 21, 2008 at 10:15 PM, Justin A. Lemkul jalem...@vt.edu wrote: Chitrita Dutta Roy wrote: tar -zxvf

Re: [gmx-users] Parallel run on a Quad Core

But one thing as i did make links so definitely there are links of those executables in /usr/local/bin.How can i easily remove them..?? On Sun, Dec 21, 2008 at 10:15 PM, Justin A. Lemkul jalem...@vt.edu wrote: Chitrita Dutta Roy wrote: tar -zxvf openmpi-1.2.8.tar.bz2 cd openmpi-1.2.8

Re: [gmx-users] Problem with trjcat -demux

I followed up by trying trjcat version 3.3.3, which I have installed in a different location. By issuing the same command, it gives another (different) error: Read 9 sets of 500 points, dt = 2 Reading frame 130 time 30.000 --- Program

Re: [gmx-users] Parallel run on a Quad Core

Justin A. Lemkul wrote: Chitrita Dutta Roy wrote: tar -zxvf openmpi-1.2.8.tar.bz2 cd openmpi-1.2.8 ./configure make make install i had my fftw library installed. untarred gromacs went to its directory.. ./configure --enable-mpi --program_suffix=_mpi make make install grompp -f pr2.mdp -c