[gmx-users] itp problem

Hello: I am trying to restrain part of my protein. First I generate a index file by make_ndx. Then I use genrest for this purpose like: genres -f npt.gro -o helix -n -fc 400 after that I change the following in the topol.top file, like: ; Include Position restraint file #ifdef POSRES #inc

Re: [gmx-users] generation of gro file

Dear Justin Again thanks. Actually the problem arises in the running of pdb2gmx of pdb file of crown ether. I have generated the pdb file from xyz coordinates using openbabel. The pdb file looks like below. COMPND D:\data-structure\18c6.xyz AUTHOR GENERATED BY OPEN BABEL 2.3.2 HETATM 1 O LIG 1

Re: [gmx-users] Lennard jones energy

On 8/17/13 4:22 PM, chinnu657 wrote: Hi all, Can someone please guide me on how I can use g_energy to print Lennard Jones energy? http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy -Justin -- == Justin A. Lemkul, Ph.D. Postdoct

[gmx-users] Lennard jones energy

Hi all, Can someone please guide me on how I can use g_energy to print Lennard Jones energy? Thank you so much in advance. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/Lennard-jones-energy-tp5010564.html Sent from the GROMACS Users Forum mailing list archive at N

Re: [gmx-users] generation of gro file

On 8/17/13 10:58 AM, Musharaf Ali wrote: Thank You Justin But you mean to say that even XYZ coordinates like below format (18-crown-6) can be directly used in Gromacs. I don't know. I seem to recall some discussion about .xyz files some time ago, but I forget the outcome. My point was tha

Re: [gmx-users] generation of gro file

Thank You Justin But you mean to say that even XYZ coordinates like below format (18-crown-6) can be directly used in Gromacs. O 0.00 0.00 0.00 C 0.00 0.00 1.40 C 1.367075 0.00 1.883328 H -0.513360 0.889165 1.763000 H -0.513360 -0.889165 1.763000 H 1.367079 0.0

[gmx-users] Problem in Gyrate analysis

Hello, I performed 20ns MD simulations on Protein-Ligand Complex. Now i tried to analysis this complex using g_gyrate. Used following command g_gyrate -s MD_first10.tpr -f File.xtc -n index.ndx -o ligand.xvg I Choose Ligand group but it gives this following error.. *** glibc detected *** g_gyr

Re: [gmx-users] generation of gro file

On 8/16/13 10:50 PM, Musharaf Ali wrote: Hi could somebody help how to generate grow file from xyz coordinates specially for crown ether type molecules. The specifications of the .gro format are described here: http://manual.gromacs.org/online/gro.html Note that there is no requirement to u

Re: [gmx-users] Regarding TCoupling and position restraints

On 8/17/13 12:10 AM, HANNIBAL LECTER wrote: Thanks. Is there any way to position restraint a part of the system while keeping all bonds flexible? Sure. Apply position restraints as normal and set "constraints = none" in the .mdp file. This will affect your choice of dt, though, and SETTLE