[gmx-developers] Water innerloop

[David van der Spoel]

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?

Can you provide a charm tip3p.itp file?


> 
> 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
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> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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