[gmx-users] TIP3P versus SPC?

[David van der Spoel]

On Tue, 2003-02-18 at 03:17, Michael Shirts wrote:
> 
> Hi, all - I was just wondering about the differences of implementation of
> TIP3P and SPC in GROMACS.  I get a couple of odd things - below are outputs of
> g_energy from two simulations, identical conditions except that one has TIP3P
> and the other has SPC.  PME, rlist = rcoulomb = 1.15, Switched VdW 0.9-1.1,
> dispersion correction, 900 molecules, Nose-Hoover, Parrinello-Rahman.
> 
> The densities remain close to the experimental values, but the coulombic
> energy for TIP3P is 20x that of SPC. Do you have any idea why this is the
> case?  It just seems rather odd that this differece in coulombic energy should
> exist without there being other large differences in other properties. . .
> 
Weird. Must be a problem in the input. Could you send me the
.itp/top/gro/mdp files?

> Thanks,
> Michael Shirts
> Pande Group
> Chemistry Department
> Stanford University
> 
> SPC with PME
> LJ (SR)                     6464.53    259.014    259.007 0.00642346    6.42347
> Disper. corr.              -162.668    1.73525    1.73521 -3.73529e-05 -0.0373529
> Coulomb (SR)               -41653.8    560.793    560.781 -0.0128294   -12.8294
> Coulomb (LR)               -2074.37    11.5334    11.5334 0.000108335   0.108336
> Potential                  -37426.3    386.944    386.939 -0.00633505   -6.33507
> Kinetic En.                 6690.03    208.658    208.657 -0.00205789    -2.0579
> Total Energy               -30736.3     542.66    542.655 -0.0083929   -8.39292
> Temperature                 298.008    9.29468    9.29464 -9.16688e-05  -0.091669
> Pressure (bar)              2.36887    478.957    478.956 0.00256479    2.56479
> Box-X                       3.02334    0.01077  0.0107698 -2.24437e-07 -0.000224437
> Volume                      27.6361   0.295627   0.295621 -6.05586e-06 -0.00605588
> Density (SI)                974.335    10.3936    10.3934 0.000223733   0.223733
> Heat Capacity Cv:        12.49 J/mol K (factor = 0.00097278)
> Isothermal Compressibility: 7.68593e-05 /bar
> Adiabatic bulk modulus:        13010.8  bar
> 
> TIP3P with PME
> LJ (SR)                      5566.8     248.61    248.593  0.0111267    9.92947
> Disper. corr.              -155.928    1.80238    1.80221 -9.61068e-05 -0.0857659
> Coulomb (SR)                -606615    584.342     584.33 -0.0142947   -12.7567
> Coulomb (LR)                -199772    11.8148    11.8148 3.28827e-05  0.0293446
> Potential                   -800976     419.16    419.159 -0.00323129   -2.88361
> Kinetic En.                 6690.07    224.102    224.099 -0.00426235   -3.80373
> Total Energy                -794286    595.936    595.933 -0.00749363   -6.68733
> Temperature                 298.009    9.98263    9.98251 -0.000189867  -0.169437
> Pressure (bar)              2.35245    467.995    467.966   0.020043    17.8864
> Box-X                       3.01574  0.0116386  0.0116374 -6.4277e-07 -0.000573609
> Volume                      27.4285   0.317837   0.317804 -1.78581e-05 -0.0159366
> Density (SI)                 981.73    11.3478    11.3468 0.000605091   0.539984
> Heat Capacity Cv:      12.4928 J/mol K (factor = 0.0011221)
> Isothermal Compressibility: 8.95143e-05 /bar
> Adiabatic bulk modulus:        11171.4  bar
> 
> Cheers,
> Michael
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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