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
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.
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
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
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!
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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 ;
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
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