[gmx-developers] Water innerloop
David van der Spoel
spoel at xray.bmc.uu.se
Tue Feb 28 08:49:32 CET 2006
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.
> 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:
>>> 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...
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> 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
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-developers-request at gromacs.org.
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
More information about the gromacs.org_gmx-developers