Errors in Installing Gromacs 4.5 in Windows 7 with Cygwin

-

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-threads --with-fft=fftw3 CPPFLAGS="-I/cygdrive/c/cygwin64/home/user/software/fftw-3.3.4/include" LDFLAGS="-L/cygdrive/c/cygwin64/home/user/software/fftw-3.3.4/lib" --enable-float --disable-mpi --without-xml
$ make -j 4

The error massage is as following:
and 


After searching online, some people suggest should re-install fftw 3 with --enable-shared. But I tried this and failed again but with different error massages.

Comments

Post a Comment

Popular posts from this blog

Fixing bugs in FF14SB port for Gromacs

-
Bugs? The newly released amber14sb made modifications for protein, DNA and RNA. This force field could be ported into gromacs as I already introduced previous. However, there are some small bugs in the improper dihedral angles of HID, HIE and HIP. So when generating tpr file, errors would be prompted. When run grompp -f npt.mdp -p topol.top -c protein.gro -o product.tpr -n index, errors occur: ERROR 1 [file topolff14sb_Protein_chain_B.itp, line 208041]:   No default Improper Dih. types The reason is that the parameters for some dihedral angles are missing. So we need to fix this. How to fix? Add the following two lines in the ffbonded.itp after the 730th lines: NA  CW  CC  CT       4      180.00     4.60240     2     ;;; HID force field added NA  CV  CC  CT       4      180.00     4.60240     2     ;;; HID force fie...
Read more

A step-by-step tutorial to perform PCA with Gromacs MD trajectory

-
Image
A step-by-step tutorial to perform PCA with Gromacs MD trajectory It is a common practice to perform principal component analysis to explore the transitions and dynamics of macromolecules simulations.   There may exist multiple states in the free energy landscape, so it is important to extract the representative structures from the energy minima in the free energy surface. To generate such a free energy surface, we could define some collective variables (CVs). However, due to the high dimensionality of the simulation trajectory, it is not always straightforward to select several more important CVs. So the problem is how could we find one or two CVs which could describe the slow motions of the system? To this end, PCA-based dimension reduction and projections could partially solve the problem by transforming the original dataset and grasp the largest variance of the system. Although there has been a tool in Gromacs, which perform the PCA using g_covar and g_anaeig...
Read more

Install new amber force fields ports in Gromacs

-
Image
Amber force fields are popular for protein, DNA, RNA and lipid simulations. Recently updated amberff12, amberff14 and amberff15 were reported to perform better than amber99sb and amber99sb-ildn. Gromacs is a commonly used simulation software, which using OpenMM to enable GPU acceleration. Gromacs is fast and easy to use. A lot of people use amberff in Gromacs. So to use the newly release amberff12 and amber14sb in gromacs, we need to some work. Step 1. Install Gromacs 4.6.x or Gromacs 5.0.x or Gromacs 5.1.x Installation instructions could be find here: For 4.6.x http://www.gromacs.org/Documentation/Installation_Instructions_4.6 For 5.0.x and 5.1.x http://www.gromacs.org/Documentation/Installation_Instructions_5.0 Suppose you are user john, you installed a gromacs 4.6.7 in /home/john/applications/. After installation, you should source the GMXRC by: source  /home/john/applications/gromacs.4.6.7/GMXRC And add topology files to environments by: export GMXLIB=/home/joh...
Read more