[gmx-users] TIP5P and cg minimization
nextgame at hotmail.com
Fri Mar 7 05:55:25 CET 2008
Jestin,I am just using the TIP5P parameter file that comes with gromacs and it doesn't have the flexible parameters in there. I too wonder the impacts it would have on MD, so maybe somebody else might have some insights. But my understanding is that the important parts of the water model are the charge, epsilon and sigma of each atom, so it is mostly these parameters that defines how accurate the water model is. The difference b/w "flexible" and "rigid" is just how you keep the water molecules together during simulation so they still adopt the right bond lengths and angles. Whether you use forces (flexible) or SHAKE (rigid), it shouldn't have too much of a dramatic impact under normal circumstances. Although, I could imagine that the impact might be significant under high temperature or something. Just by searching through the mailing list, it doesn't seem to be a concern and I am sure plenty of people have used the same TIP5P parameter file. At least this is how I convinced myself to not worry so I can sleep at night, anyways. -Rob
Date: Fri, 7 Mar 2008 01:15:25 +0000From: jesbman at rediffmail.comTo: gmx-users at gromacs.orgCC: nextgame at hotmail.comSubject: Re: RE: [gmx-users] TIP5P and cg minimization Rob,I wonder whether you have got the flexible water model, TIP5P. I want to run simulations using the flexible TIP5P water model. Well, how does the results from the MD be affected if I use rigid water models in place of a flexible one?regardsJestinOn Thu, 06 Mar 2008 rob yang wrote :>>Thanks Mark for the pointer.>>The TIP5P.itp has [settles] only, whereas TIP4P.itp (as well as spc.itp, and TIP3P) has parameters for flexible water [FLEXIBLE] as well as rigid [settles]. This, by definition would restrict any systems using TIP5P to the SHAKE algorithm. I am wondering:>1) are there other TIP5P.itp files that possibly include the FLEXIBLE parameters (force constants for bonds and angles)?>2) for my present TIP5P.itp, is this going to impact the MD run?>
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