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AmberTools 16 together with Ipython notebook Amber (starting from 16) supports Ipython notebook (also known as jupyther notebook), which is useful for trajectories visulization and analysis and is very powerful tool to record your commands.  Besides the amber mdcrd trajectories, you may also use it to analyze your gromacs trajectories.  The strength of IPython notebook is that it is flexible and extendable and very user-friendly.  In case you'd like to try IPython notebook together with MD trajectory analysis, you could first read few pages about Jupyter notebook and AMBER pytraj. http://jupyter.org/ http://ambermd.org/tutorials/analysis/tutorial_notebooks/nglview_notebook/ http://ambermd.org/tutorials/analysis/ If you'd like to use it, these are useful step-by-step instructions for Pytraj with Ipython here : You need to install conda or anaconda first. See this link   https://docs.continuum.io/anaconda/install 1. login to ...

There are some bugs when running GOLD 5.4 in parallel with PVM (parallel virtual machine). In the "intcor", there is not value reported in the final docking result file "bestranking.lst". Run-1: In parallel with PVM using 8 cpus (parallel_gold_li*) ============================== ====================== #     Fitness  S(hb_ext) S(vdw_ext)  S(hb_int)    S(int)      intcor      time                               File name                Ligand name        46.25       9.00       27.86              0.00      -1.06       ----         15.870    './ligands_ m1_2.mol2'    'ligand_001' ============================== ====================== If running...

Well, I am a Gromacs user, I am thinking about installing gromacs in windows, thus I could do some simple analysis more easily since my daliy work is all in Win 7 and SSH shell. So I did some research online, and found some websites talking about this topic. But I didnit find a very clear way to do so. Then I tried to install Gromacs 4.5.5 by myself in my HP Prodesk, which has Win 7 64-bit OS with Cygwin. Firstly, I tried to install FFTW 3.3.4, and things went quick well. $ tar zxvf fftw-3.3.4.tar.gz $ cd fftw-3.3.4 $ ./configure --prefix=/cygdrive/c/cygwin64/home/user/software/fftw-3.3.4 --enable-float --enable-shared $ make $ make install So far, everything was okay. Then, I downloaded Gromacs-4.5.5.tar.gz and copy to installation folder. And I unzip it and configure it, following by  "make -j 4", which gave me errors. Thus I added some commands in ./configure step. Later, I tried the following commands and still some error massage. $./configure --disable-...