Skip to content
Snippets Groups Projects
Commit c6f24ba0 authored by carlocamilloni's avatar carlocamilloni
Browse files

fix in docs

parent 66abe4d7
No related branches found
No related tags found
No related merge requests found
......@@ -36,7 +36,7 @@ account the agreement with the experimental data considering the multiple source
\section isdb-1-reference Run a reference simulation
The system we use is the EGAAWAASS peptide used in ref. \cite Lohr:2017gc .
First of all we will run a simulation in implicit solvent using the EEF1-SB CHARMM36 force field. EEF1-SB includes a correction to the standard backbone torsion potentianl of CHARMM36, an electrostatic interaction with a distance dependent dielectric constant and a simple gaussian form for the solvation energy. The first two terms are implemented in the force field and using table potentials while the latter is implemented as a collective variable in PLUMED, \ref IMPLICIT .
First of all we will run a simulation in implicit solvent using the EEF1-SB CHARMM36 force field. EEF1-SB includes a correction to the standard backbone torsion potentianl of CHARMM36, an electrostatic interaction with a distance dependent dielectric constant and a simple gaussian form for the solvation energy. The first two terms are implemented in the force field and using table potentials while the latter is implemented as a collective variable in PLUMED, \ref EFFSOLV .
\plumedfile
# this is optional and tell to VIM that this is a PLUMED file
......@@ -47,7 +47,7 @@ WHOLEMOLECULES ENTITY0=1-111
# EEF1SB Implicit solvation
protein-h: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein-H
solv: IMPLICIT ATOMS=protein-h NOPBC NL_STRIDE=10 NL_BUFFER=0.1
solv: EFFSOLV ATOMS=protein-h NOPBC NL_STRIDE=10 NL_BUFFER=0.1
bias: BIASVALUE ARG=solv
\endplumedfile
......
......@@ -6,7 +6,7 @@ WHOLEMOLECULES ENTITY0=1-111
# EEF1SB Implicit solvation
protein-h: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein-H
solv: IMPLICIT ATOMS=protein-h NOPBC NL_STRIDE=10 NL_BUFFER=0.1
solv: EFFSOLV ATOMS=protein-h NOPBC NL_STRIDE=10 NL_BUFFER=0.1
bias: BIASVALUE ARG=solv
# CVs, Psi9, Phi1 are not defined
......
......@@ -6,7 +6,7 @@ WHOLEMOLECULES ENTITY0=1-111
# EEF1SB Implicit solvation
protein-h: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein-H
solv: IMPLICIT ATOMS=protein-h NOPBC NL_STRIDE=10 NL_BUFFER=0.1
solv: EFFSOLV ATOMS=protein-h NOPBC NL_STRIDE=10 NL_BUFFER=0.1
bias: BIASVALUE ARG=solv
# CVs, Psi9, Phi1 are not defined
......
......@@ -6,7 +6,7 @@ WHOLEMOLECULES ENTITY0=1-111
# EEF1SB Implicit solvation
protein-h: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein-H
solv: IMPLICIT ATOMS=protein-h NOPBC NL_STRIDE=10 NL_BUFFER=0.1
solv: EFFSOLV ATOMS=protein-h NOPBC NL_STRIDE=10 NL_BUFFER=0.1
bias: BIASVALUE ARG=solv
PRINT FILE=ENERGY ARG=bias.bias STRIDE=200
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment