[gmx-users] installing Gromacs4.6.3 on cygwin

2013-09-08 Thread shahid nayeem
Dear all I am installing gromacs -4.6.3 on cygwin with following commands tar -xvzf gramcs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on It runs fine and write file in build directory. when I run make command it gives following error. [ 15%]

[gmx-users] GaussView 4.0 and ITP adjuster

2013-09-08 Thread MUSYOKA THOMMAS
Dear Users, I am trying to run Protein-Ligand MD simulations using GROMACS. However, i seem to be lost in building correct ligand topologies. I came across an article explaining that the above mentioned softwares can be used to build a ligand topology file that can act as a guide in allocating

Re: [gmx-users] NMR restrained MD

2013-09-08 Thread Mark Abraham
... and probably the use of grompp -maxwarn 5 is hiding problems that you should be fixing first! Mark On Sun, Sep 8, 2013 at 1:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/7/13 6:55 PM, Rama Krishna Koppisetti wrote: Hi Justin, If you are willing to see my complex pdb file or complex

[gmx-users] g_polystat: eigenvectors of the gyration tensor

2013-09-08 Thread gtesei
Dear all, Using g_polystat with option -v, I obtain the output file polyvec.xvg which contains 10 columns. Are columns 2-10 the components of the gyration tensor calculated according to this definition http://en.wikipedia.org/wiki/Gyration_tensor ? If this is correct, are the components

RE: [gmx-users] g_current

2013-09-08 Thread Nilesh Dhumal
Did you get chance to take look at the g_current? why it is -inf (infinity) at the end with -mc option (mc.xvg). -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, July 09, 2013 5:06 AM To: