[gmx-users] coarse-grained simulation of proteins

Hi, everyone. I'm trying a coarse-grained simulation with three beads representing the backbone structure of each residue. However, it's difficult to get the LJ parameters for -NH- and -CO- . Could anyone possibly know some work on this? Thanks in advance. Cristty __

[gmx-users] g_energy to compute free energy difference

Dear users, As the Gromacs manual mentioned, "g_energy" cauld calculate the free energy difference with an ideal gas state. After a simulation of protein in water with GMX3.3.1, I have tried the following commands to compute deltaG. 1. g_energy -f md.edr -fee -fetemp 300 -o energy1.xvg 2. g

[gmx-users] how to calculate redisue wise RMSD in gromacs?

Dear friends, I have carried out a simulation of a protein in solution and want to analyse redisue wise root-mean-square-deviation (RMSD) of the protein. As far as I know, RMSD can be calculated by g_rms, which gives RMSD as a function of time, but what I expect is RMSD as a function of residue

[gmx-users] MPICH 1.2 vs. GMX 4.0

I often had problems when running GMX 3.3 on mpich-1.2.x , to be exactly, the simulations always crash when running on more than 5 cores. I wonder whether this can be fixed in GMX 4.0. Sincerely yours, Ying Ren 2008-02-29 State Key Laboratory of Mult

[gmx-users] GMX compilation with "--enable-threads"

Many thanks to Mark. When "--enable-threads" is omited,the compilation seems to be fine but "mdrun" can not run in parallel,e.g. trying to run on 6 nodes: grompp -np 6 . mpirun -np 6 Fatal error: run input file md.tpr was made for 6 nodes,while mdrun_d expected it to be for 1 nodes

[gmx-users] GMX compilation with "--enable-threads"

Hello, everyone! I try to install gromacs 3.3.1 with threads enabled. But it fails and gives the following info: ... /opt/mpich/bin/mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o grompp topio.o toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o