From c6f24ba00d0af56caacc071771111cb3c3ee701b Mon Sep 17 00:00:00 2001 From: carlocamilloni <carlo.camilloni@gmail.com> Date: Fri, 8 Sep 2017 09:17:17 +0200 Subject: [PATCH] fix in docs --- user-doc/tutorials/others/isdb-1.txt | 4 ++-- .../others/isdb-1/m_and_m/plumed-eef1-pbmetad-m_m.dat | 2 +- .../isdb-1/reference-impl-pbmetad/plumed-eef1-pbmetad.dat | 2 +- .../tutorials/others/isdb-1/reference-impl/plumed-eef1.dat | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/user-doc/tutorials/others/isdb-1.txt b/user-doc/tutorials/others/isdb-1.txt index 98b5fad80..bc8080852 100644 --- a/user-doc/tutorials/others/isdb-1.txt +++ b/user-doc/tutorials/others/isdb-1.txt @@ -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 diff --git a/user-doc/tutorials/others/isdb-1/m_and_m/plumed-eef1-pbmetad-m_m.dat b/user-doc/tutorials/others/isdb-1/m_and_m/plumed-eef1-pbmetad-m_m.dat index 17029337b..1983e1281 100644 --- a/user-doc/tutorials/others/isdb-1/m_and_m/plumed-eef1-pbmetad-m_m.dat +++ b/user-doc/tutorials/others/isdb-1/m_and_m/plumed-eef1-pbmetad-m_m.dat @@ -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 diff --git a/user-doc/tutorials/others/isdb-1/reference-impl-pbmetad/plumed-eef1-pbmetad.dat b/user-doc/tutorials/others/isdb-1/reference-impl-pbmetad/plumed-eef1-pbmetad.dat index f9a194f6f..a388be1d7 100644 --- a/user-doc/tutorials/others/isdb-1/reference-impl-pbmetad/plumed-eef1-pbmetad.dat +++ b/user-doc/tutorials/others/isdb-1/reference-impl-pbmetad/plumed-eef1-pbmetad.dat @@ -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 diff --git a/user-doc/tutorials/others/isdb-1/reference-impl/plumed-eef1.dat b/user-doc/tutorials/others/isdb-1/reference-impl/plumed-eef1.dat index eebf8c5db..4a6760c48 100644 --- a/user-doc/tutorials/others/isdb-1/reference-impl/plumed-eef1.dat +++ b/user-doc/tutorials/others/isdb-1/reference-impl/plumed-eef1.dat @@ -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 -- GitLab