TIP4P topology and parameter files

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Sun Apr 19 2015 - 05:18:41 CDT

Dear NAMD Users,
I want to use TIP4P water model in order to perform bulk water md simulations. So I searched for TIP4P topology and parameter files for NAMD. And I found two different tpg and prm file sets. These files can be seen in below. When I compared these files, I realized that values and structures in these tpg and prm files are not the same. Because of this I couldn’t decide which tpg and prm files are right for TIP4P water model. Could you please help me to chose the right tpg and prm files for NAMD ?
Thanks for the help.
1 -  toppar_water_ions_tip4p.str
TPG FILE:
* Charmm topology file31  1

MASS  1   HT    1.00800 H  ! TIPS3P WATER HYDROGENMASS  2   OT   15.99940 O  ! TIPS3P WATER OXYGEN, TIP4PMASS  3   LP    0.00000 H ! virtual particle for M-site/lone pairs
default first none last none
RESI TIP4         0.000 ! tip4p water model, generate using noangle nodihedral
GROUPATOM OH2  OT      0.0ATOM OM   LP     -1.04ATOM H1   HT      0.52ATOM H2   HT      0.52BOND OH2 H1 OH2 H2 H1 H2    ! the last bond is needed for shakeBOND OH2  OMANGLE H1 OH2 H2             ! requiredACCEPTOR OH2!DONOR H1 OH2!DONOR H2 OH2LONEPAIR bisector OM OH2 H1 H2  distance 0.15 angle 0.0 dihe 0.0IC   H1   OM   *OH2   H2    0.9572   52.26  180.00   52.26   0.9572IC   H2   H1    OH2   OM    0.0000    0.00    0.00   52.26   0.15PATCHING FIRS NONE LAST NONE
END
PRM FILE:
BONDS
!V(bond) = Kb(b - b0)**2!Kb: kcal/mole/A**2!b0: A!atom type Kb          b0
HT    HT      0.0       1.5139  ! from TIPS3P geometry (for SHAKE w/PARAM)HT    OT    450.0       0.9572  ! from TIPS3P geometryOT    LP      0.0       0.15    ! from TIP4P  geometry

ANGLES
!V(angle) = Ktheta(Theta - Theta0)**2!V(Urey-Bradley) = Kub(S - S0)**2!Ktheta: kcal/mole/rad**2!Theta0: degrees!Kub: kcal/mole/A**2 (Urey-Bradley)!S0: A!atom types     Ktheta    Theta0   Kub     S0

HT   OT   HT     55.0      104.52   ! FROM TIPS3P GEOMETRY
 NONBONDED
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j!atom  ignored    epsilon      Rmin/2   ignored   eps,1-4       Rmin/2,1-4

HT       0.0       -0.0       0.0OT       0.0       -0.155     1.7699LP       0.0       -0.00      0.0

END
*********************
http://www.ks.uiuc.edu/~petefred/tip4p-kit.tbz
TPG FILE:
* TIP4P WATER TOPOLOGY FILE*   18    1MASS     4 HT     1.00800 ! TIPS3P WATER HYDROGENMASS    58 OT    15.99940 ! TIPS3P WATER OXYGENMASS    89 LP     0.00000 ! TIPS3P WATER OXYGEN CHARGE CENTER
RESI TIP4    0.00   ! TIPS4P WATER MODELGROUPATOM OH2  OT      0.00ATOM H1   HT      0.52ATOM H2   HT      0.52ATOM OM   LP     -1.04BOND OH2  H1     OH2  OM    OH2  H2ANGLE H1   OH2  H2ANGLE H1 OH2 OMANGLE H2 OH2 OM
IC   H1   OH2   OM    H2    0.9572   52.26  180.00   60.13   0.8731IC   H2   H1    OH2   OM    1.5139   37.74  180.00   52.26   0.15
PATC  FIRS NONE LAST NONE
! you will need to invoke a command such as:!    LONEpair BISEctor DIST 0.15 ANGLE 0.0 DIHE 0.0 -!            SELE ATOM SOLV * OM  END  SELE ATOM SOLV * OH2 END - !            SELE ATOM SOLV * H1  END  SELE ATOM SOLV * H2  END! to create the lonepairsEND
PRM FILE:
* TIP4P WATER PARAMETER FILE*BONDHT   OT     450.0       0.9572 ! from TIP4P geometryHT   HT       0.0       1.5139 ! from TIP4P geometry (for SHAKE w/PARAM)LP   OT     450.0       0.15   ! from TIP4P geometry
ANGLESHT   OT   HT      55.0     104.52    ! FROM TIP4P GEOMETRYHT   OT   LP      50.0      52.26!HT   OT   LP      0.1      52.26!NONB! We use the standard TIP4P oxygen vdw parameters, and the hydrogen ! parameters from TIP3P as used in charmm. This means the NBFIX is not! needed. This can be changed for mixed systems.HT       0.0000     0.0000    0.0250 !TIP3P water hydrogen, see NBFIX belowOT       0.0000    -0.1550    1.7701 !TIP3P water oxygen,   see NBFIX belowLP       0.0000     0.0000    0.0000 ! TIP4P lone pair
END

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