RE: [gmx-users] g_rdf -surf

2012-02-12 Thread Payman Pirzadeh
Hello, Thanks for your attention. A word was missing in my previous e-mail!! The g(r) is NOT normalized. Here was my command: g_rdf -f traj.xtc -s topol.tpr -n reidues_atoms.ndx -o gofr -surf res The index file includes atoms in the side chain exposed to the solvent: [ SideChain_&_r_13

Re: [gmx-users] g_rdf -surf

2012-02-12 Thread Mark Abraham
On 13/02/2012 5:54 PM, Payman Pirzadeh wrote: Hello, I am trying to calculate the RDF of water next to surface of certain residues. I used the an index file which includes the residues as the first group, and the #12 option (SOL) in the g_rdf, and used the option '--surf res' on the prompt.

RE: [gmx-users] g_rdf -surf

2012-02-12 Thread Payman Pirzadeh
Hello, I am trying to calculate the RDF of water next to surface of certain residues. I used the an index file which includes the residues as the first group, and the #12 option (SOL) in the g_rdf, and used the option '-surf res' on the prompt. However, the calculated RDF rises up to 41000 in long

Re: [gmx-users] charmm-gui and gromacs

2012-02-12 Thread Mark Abraham
On 13/02/2012 12:15 PM, xiaojiong wrote: Dear: If I have used the charmm-gui to build the bilayer for the receptor-ligand complex,can I load the outcome to the gromacs to perform MD?Is the process complicated? How do it? Thanks! You can probably write a .pdb coordinate file from any tool

[gmx-users] charmm-gui and gromacs

2012-02-12 Thread xiaojiong
Dear: If I have used the charmm-gui to build the bilayer for the receptor-ligand complex,can I load the outcome to the gromacs to perform MD?Is the process complicated? How do it? Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] gibbs+umbrella+constraint

2012-02-12 Thread parto haghighi
Dear gmx users I am working on an umbrella sampling system.(lipid bilayer+drug). I have used distance here is my mdp file for pulling: title = Umbrella pulling simulation define = -DPOSRES_LIP ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 250 ;

[gmx-users] RE:dhdl calculations

2012-02-12 Thread lloyd riggs
Dear All, Does anyone know the equation used to calculate the dH and dH/dl in free energy calculations via gromacs (other than looking at code that looks like 3*pi/(pi-.). That or the actual reference for it. I found a couple references for the gromacs use of the free energy but none hav