[gmx-developers] Water innerloop

[Yang Ye]

David van der Spoel wrote:
> Yang Ye wrote:
>> Hi, Mark
>>
>> This is from CHARMM22 paper (JPC, B, 1998, 102: 3586) page 3588
>>
>> The water model used in all calculations is the TIP3P model (20) 
>> modified for the CHARMM force field.(5) The consistency of the 
>> protein and solvent interactions is based on the use of this water 
>> model; i.e., it forms part of the system description and other water 
>> models would be less appropriate.
>>
>> Reference (5) is Reiher, W. E., III. Ph.D. Thesis, Harvard 
>> University, 1985. I cannot got it.
>>
>> And if you check CHARMM22, 27, HT in TIP3P does have LJ defined, 
>> which is different from original TIP3P.
>>
>> Also check here. 
>> http://www.cs.sandia.gov/~sjplimp/lammps/doc/Section_howto.html#4_7 
>> <http://www.cs.sandia.gov/%7Esjplimp/lammps/doc/Section_howto.html#4_7>
>>
>> So, two questions:
>> 1. What's the impact of using original TIP3P water?
>> 2. What can be done in GROMACS to accelerate CHARMM's TIP3P water?
>
> How large is the difference in performance?
With a system of 13470 water, 102.708 hr/ns for CHARMM TIP3P and 61.277 
hr/ns for normal TIP3P.

The first few lines of the summary for CHARMM TIP3P

 Computing:                        M-Number         M-Flops  % of Flops
-----------------------------------------------------------------------
 VdW(T)                         1857.684230   100314.948420     0.0
 Coul(T)                      530346.478611 22274552.101662     4.6
 Coul(T) + VdW(T)            4492147.365459 305466020.851212    62.9
 Outer nonbonded loop          33007.755743   330077.557430     0.1
 1,4 nonbonded interactions      716.102387    64449.214830     0.0

All TIP3P water is regarded as normal molecules.
> Can you provide a charm tip3p.itp file?
It is identical to AMBER's.

[ moleculetype ]
; molname       nrexcl
SOL             1

[ atoms ]
; id    at type res nr  residu name     at name         cg nr   charge
1       OT      1       SOL             OW              1       -0.834
2       HT      1       SOL             HW1             1       0.417
3       HT      1       SOL             HW2             1       0.417
[ settles ]
; i     j       funct   length
1       1       0.09572 0.15139
[ exclusions ]
1       2       3
2       1       3
3       1       2

The difference is in the LJ definition of HT and OT

comb-rule 1
    HT     1.008     0.000     A  3.1539699357e-09  1.2921281844e-17
    HW     1.008     0.000     A  0.0000000000e+00  0.0000000000e+00

    OT    15.999     0.000     A  2.4895403920e-03  2.4347673691e-06
    OW    15.999     0.000     A  2.4887479484e-03  2.4348183991e-06

So it is natural for CHARMM TIP3P is not recognized feasible for water 
innerloop.
>> Yang Ye
>>
>> Mark Abraham wrote:
>>> Yang Ye wrote:
>>>> Hi,
>>>>
>>>> Is there any technique to accelerate computation for CHARMM TIP3P 
>>>> water of which H has LJ interactions?
>>>
>>> I didn't think TIP3P had LJ interactions. Am I wrong? CHARMM 
>>> forcefields are optimized for TIP3P solvent, but the papers imply 
>>> it's standard TIP3P...
>>>
>>> Mark
>>> _______________________________________________
>>> gmx-developers mailing list
>>> gmx-developers at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-developers
>>> Please don't post (un)subscribe requests to the list. Use the www 
>>> interface or send it to gmx-developers-request at gromacs.org.
>>>
>>
>>
>> _______________________________________________
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-developers-request at gromacs.org.
>
>
>