Re: [gmx-users] template.c

Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote: Thank you very much for your suggestion... The problem is the voronoi generator program was written in C++ as a win32 application. It is heavily object-oriented and to my current level of programming would be very hard to compile in Linux.

Re: [gmx-users] template.c

Thank you very much for your suggestion... The problem is the voronoi generator program was written in C++ as a win32 application. It is heavily object-oriented and to my current level of programming would be very hard to compile in Linux. Regards. Pedro. 2007/6/8, David van der Spoel <[EMAIL P

[gmx-users] g_chi -all

I'm trying to plot the chi angle of a specific a.a. residue as a function of time. To do this, I'm trying to use the -all flag and I'm having trouble generating any output files. Prior to trying -all, I successfully created chi.log, order.xvg and dihcorr.xvg files. The current command I am usin

Re: [gmx-users] template.c

Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote: Hi, I'm trying to use "template.c" so as to make my own analysis tool for gmx-generated trajectories. Due to the complexity of the tool (it builds an affine Voronoi diagram), I want to compile it as a stand-alone application. Unfortunatel

[gmx-users] template.c

Hi, I'm trying to use "template.c" so as to make my own analysis tool for gmx-generated trajectories. Due to the complexity of the tool (it builds an affine Voronoi diagram), I want to compile it as a stand-alone application. Unfortunately, the compiler cannot resolve several external functions c

Re: [gmx-users] AIX 5.3 compilation error

Marius Retegan wrote: Dear Gromacs users, I have problems compiling Gromacs on a IBM cluster P575 with Power5 cpus. I've used this flag for compilation == #!/bin/ksh #export MPICC='mpcc_r -q64' export AR='ar -X 64' export CC='xlc_r -q64' export F77='xlf_r -q64' exp

Re: [gmx-users] Fwd: Individual energies of amino acids

abhigna polavarapu wrote: Hi Mark, I need to calculate the individual energies of aminoacids using Gromacs. But while using energygrps option in .mdp file for each amino acid I can only calculated the nonbonded energies of this residue. Is there a way where I can calculated th

[gmx-users] Fwd: Individual energies of amino acids

Hi Mark, I need to calculate the individual energies of aminoacids using Gromacs. But while using energygrps option in .mdp file for each amino acid I can only calculated the nonbonded energies of this residue. Is there a way where I can calculated the bonded interactions for each ami

Re: [gmx-users] adding counter ions

Not for the sake of the PME, since your system has no net charge. However, there a few papers out there discussing the need for counterions for proper folding and such. /Erik 8 jun 2007 kl. 13.11 skrev OZGE ENGIN: Hi all, My peptide contains two adversely charged residues. I use PME opt

[gmx-users] adding counter ions

Hi all, My peptide contains two adversely charged residues. I use PME option for the investigation of electrostatic interactions within my system. The total charge of the box must be neutral. Since the system contains adversely charged residues, is it still necessary to add counter ions into th

[gmx-users] AIX 5.3 compilation error

Dear Gromacs users, I have problems compiling Gromacs on a IBM cluster P575 with Power5 cpus. I've used this flag for compilation == #!/bin/ksh #export MPICC='mpcc_r -q64' export AR='ar -X 64' export CC='xlc_r -q64' export F77='xlf_r -q64' export CXX='xlC_r -q64' ex