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
*********************
2 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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