Add methanol and TIP4P water model

msoroush · Aug 30, 2019 · 3e2d40a · 3e2d40a
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diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # FreeEnergy
 This repository is a bash script to prepare the simulation files for absolute FreeEnergy calculation using TI and FEP methods in GOMC.
-GOMC currently bias LJ and Coulombic interaction with lambda, using soft-core or hard-core scheme, as implemented in GROMACS. For more details regarding the biasing scheme, please refer to [GROMACS Documentation](http://manual.gromacs.org/documentation/2019/reference-manual/functions/free-energy-interactions.html). 
+GOMC currently bias LJ and Coulombic interaction with lambda, using soft-core or hard-core scheme, as implemented in GROMACS. For more details regarding the biasing scheme, please refer to GROMACS [Documentation](http://manual.gromacs.org/documentation/2019/reference-manual/functions/free-energy-interactions.html). 
 
 ## Software dependency:
 1. [packmol](http://leandro.iqm.unicamp.br/packmol/versionhistory/) for packing molecule in box. 
@@ -71,7 +71,7 @@ EQ_MC=2000000                                    # steps for equilibration simul
 NPT_MC=10000000                                  # steps for NPT equilibration simulation
 FE_FREQ=5000                                     # free energy calc frequency
 STATES=(0    1    2    3    4    5    6    7)    # state id (for user only) 
-VDW=(0.000 0.20 0.40 0.60 0.80 1.00 1.00 1.00)   # lambda vector for VDW
+VDW=(0.00  0.20 0.40 0.60 0.80 1.00 1.00 1.00)   # lambda vector for VDW
 COUL=(0.00 0.00 0.00 0.20 0.40 0.60 0.80 1.00)   # lambda vector for Coulomb
 ```
 

diff --git a/build/model/Topology.top b/build/model/Topology.top
@@ -23,15 +23,16 @@ MASS   6    H    1.0080 H  ! H in alcohol
 MASS   7  OH1	 15.999 O  ! O in alcohol
 MASS   8  CF2    50.000 C  ! CF2  	   
 MASS   9  CF3    69.000 C  ! CF3
-MASS  10  HO     1.0080 H  ! H in water
+MASS  10   HO     1.008 H  ! H in water
 MASS  11  OH2	 15.999 O  ! O in water
-MASS  12   HE	 4.0026 He ! He
-
+MASS  12   MO     0.000 D ! Dummy atom for TIP4P model
+MASS  13   HE	 4.0026 He ! He
 
 
 DEFA FIRS none LAST none
 AUTOGENERATE ANGLES DIHEDRALS
 
+
 RESI SPC        0.00 ! SPC water
 GROUP
 ATOM H1 HO      0.41 ! H1    H2
@@ -40,6 +41,15 @@ ATOM H2 HO      0.41 !    O2
 BOND O2 H1 O2 H2
 PATCHING FIRS NONE LAST NONE
 
+RESI TIP4          0.00 ! water TIP4P model
+GROUP
+ATOM O2  OH2       0.000 !      O
+ATOM H1  HO        0.520 !    / | \
+ATOM H2	 HO   	   0.520 !   /  M  \
+ATOM M   MO       -1.040 ! H1       H2
+BOND O2 H1  O2 H2  O2 M       
+PATCHING FIRS NONE LAST NONE
+
 RESI HE        0.00 ! helium
 GROUP
 ATOM H1  HE     0.00 ! He
@@ -151,6 +161,15 @@ BOND C13 C14 C14 C15 C15 C16
 PATCHING FIRS NONE LAST NONE
 
 
+!methanol
+RESI C1OH	  0.00
+GROUP
+ATOM H1   H     0.435 
+ATOM O1   OH1  -0.700   
+ATOM C1	  CH2   0.265   
+BOND H1 O1  O1 C1
+PATCHING FIRS NONE LAST NONE
+
 !1-octanol
 RESI C8OH	  0.00
 GROUP

diff --git a/build/model/parameter.par b/build/model/parameter.par
@@ -11,6 +11,7 @@ BONDS
 !atom type Kb          b0  All constants from Charmm
 CH2  CH2   99999999999     1.5400 ! Alkane
 CH2  CH3   99999999999     1.5400 ! Alkane
+OH1  CH3   99999999999     1.4300 ! Alcohol
 OH1  CH2   99999999999     1.4300 ! Alcohol
 OH1  H     99999999999     0.9450 ! Alcohol
 ! fluorcarbons
@@ -23,7 +24,10 @@ CH2  CF2   99999999999     1.5400
 CH2  CF3   99999999999     1.5400
 CH3  CF2   99999999999     1.5400
 !water SPC
-HO   OH2   99999999999     1.0000
+HO   OH2   99999999999     1.0000 ! OH bond in SPC
+!water TIP4P
+HO   OH2   99999999999     0.9572 ! OH bond in TIP4P
+OH2  MO    99999999999     0.1500 ! M-O bond in TIP4P
 
 ANGLES
 !
@@ -61,7 +65,10 @@ OH1  CH2  CF2   62.1    109.5
 OH1  CF2  CH3	62.1    109.5
 OH1  CF2  CH2   62.1    109.5
 !water SPC
-HO   OH2  HO   99999999999  109.47
+HO   OH2  HO   99999999999  109.47  ! Fix Angle
+!water TIP4P
+HO   OH2  HO   99999999999  104.52  ! Fix Angle
+HO   OH2  MO   99999999999   52.26  ! Fix Angle
 
 
 DIHEDRALS
@@ -179,9 +186,13 @@ CH2	0.000000    -0.091406   2.216863   0.0   0.0   0.0
 ! Fluorocarbons ! parameteres from Zhang and Siepmann JPCB 2005
 CF3	0.000000    -0.172877	2.446967   0.0   0.0   0.0			
 CF2	0.000000    -0.054645	2.654623   0.0   0.0   0.0
-! Octanol
+! alcohol
 H	0.000000     0.000000   0.000000   0.0   0.0   0.0
 OH1	0.000000    -0.184799   1.694918   0.0   0.0   0.0
 ! SPC 
 HO	0.000000     0.000000   0.0000000   0.0   0.0   0.0
 OH2	0.000000    -0.155411   1.7774185   0.0   0.0   0.0
+! TIP4P
+HO	0.000000     0.00000    0.000000    0.0   0.0   0.0
+MO      0.000000     0.00000    0.000000    0.0   0.0   0.0
+OH2	0.000000    -0.155043   1.770123    0.0   0.0   0.0
diff --git a/build/pdb/TIP4P.pdb b/build/pdb/TIP4P.pdb
@@ -0,0 +1,6 @@
+CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1           1
+ATOM      1  O2  TIP4A   1      -0.189   1.073   0.000  0.00  0.00           O
+ATOM      2  H1  TIP4A   1       0.768   1.114   0.000  0.00  0.00           H
+ATOM      3  H2  TIP4A   1      -0.469   1.988   0.000  0.00  0.00           H
+ATOM      4  M   TIP4A   1      -0.102   1.195   0.000  0.00  0.00           D
+END
diff --git a/build/pdb/methanol.pdb b/build/pdb/methanol.pdb
@@ -0,0 +1,3 @@
+ATOM      1 H1   C1OH    1       1.355  16.046  39.158  0.00  0.00            
+ATOM      2 O1   C1OH    1       1.667  16.263  38.293  0.00  0.00            
+ATOM      3 C1   C1OH    1       2.604  17.328  38.469  0.00  0.00