RE: [gmx-users] Hbonds between Adenine and Thymine

I only used pdb2gmx when I prepared the DNA which I created with nab. and the command that  I used was:  make_ndx -f md_0_1.gro  -o index.ndx after that then I press r10 and r17 I get : 14 r_10                :    64 atoms 15 r_17                :    64 atoms This are the coordinates for the

Re: [gmx-users] Hbonds between Adenine and Thymine

I answered this already: http://lists.gromacs.org/pipermail/gmx-users/2012-November/076750.html -Justin On 12/2/12 7:21 AM, Hovakim Grabski wrote: I only used pdb2gmx when I prepared the DNA which I created with nab. and the command that I used was: make_ndx -f md_0_1.gro -o index.ndx

Re: [gmx-users] Question about dihedral angle notation

On 12/1/12 1:54 PM, Andrew DeYoung wrote: Hi, I am looking at the file ffbonded.itp located in the oplsaa.ff directory (usually located in /usr/local/gromacs/share/gromacs/top/oplsaa.ff). I see the following entry in the [ dihedraltypes ] section: C3 CT OH HO 3

Re: [gmx-users] Electrostatic field in atoms - GROMACS is not reading table interaction functions for bonded interactions

Hi. Thanks for the reply. So you are saying that the topology file should look more like: [bonds] ; aiaj functc0c1c2c3 1 2 91 1 3 91 1 4 91 1 5 91 5 6 91 5

Re: [gmx-users] help

On 12/2/12 2:17 AM, 申昊 wrote: Hi everyone， I am a new one on using gromacs. Now I have some problems. [1] I want using g_analyze to calculate the self-ACF with the dist.xvg resulted from g_dist, the file nameddist.xvg consists two lists of time(ns) and distance(nm),

[gmx-users] barium ion simulation

Dear Gromacs Users, I am trying to simulate a protein in lipid bilayer with a barium ion binding pocket in it, with Charmm27 FF in gromacs 4.5.4. I found that barium ion is not included under charmm27 ff ions.itp. I was wondering if there is any way to simulate protein with barium bound using

Re: [gmx-users] barium ion simulation

You should ask the CHARMM forum to see if anyone there has derived Ba2+ parameters that can then be converted to gromacs. On 2012-12-02 02:31:27PM -0600, ram bio wrote: Dear Gromacs Users, I am trying to simulate a protein in lipid bilayer with a barium ion binding pocket in it, with

[gmx-users] Interaction energy between two molecules.

Dear Gromacs User, I am simulating two constrained fullerenes to analyze the interaction energy between these two in vacuum. To do that I specified energygrps in .mdp file as CB1 and CB2 which corrospond to the residue name of first and second fullerene respectively. The charge of the atoms of

Re: [gmx-users] Interaction energy between two molecules.

On 12/2/12 10:38 PM, Mortuza Munna wrote: Dear Gromacs User, I am simulating two constrained fullerenes to analyze the interaction energy between these two in vacuum. To do that I specified energygrps in .mdp file as CB1 and CB2 which corrospond to the residue name of first and second