[gmx-users] Re: TIP3P versus SPC?

[Michael Shirts]

So, the problem appears to be that exclusions were not defined in the
tip3pgmx.itp file included in the gromacs distribution.  Once I added
exclusions like the ones in the spc.itp file, it gave much more reasonable
(i.e., similar to spc) results.  Since I was using SETTLE, it corrected for
the large forces after each step.  Any other known errors in the .itp files
that I should be aware of?

To answer the person who was asking about SPC/E water - I don't plan on
running any comparisons, but if you REALLY want to know the answer for sure,
you should run it yourself.  Don't trust people like me who can't figure out
that the exculsions are set up wrong ;)

Correction to add to tip3pgmx.itp?
*******************
[ exclusions ]
1 2 3
2 1 3
3 1 2
********************

On Mon, 17 Feb 2003, 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. . .
>
> 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
>
>
>


Cheers,
Michael