<DIV>Hi, Eric</DIV>
<DIV> </DIV>
<DIV>the unit 1fs = how many 1ps?</DIV>
<DIV>Why use smaller timestep - 1fs ? </DIV>
<DIV><BR>Thanks!</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV><BR><B><I>Erik Lindahl <lindahl@stanford.edu></I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Hi Rui,<BR><BR><BR>On Thursday, September 11, 2003, at 08:28 PM, qiao rui wrote:<BR><BR>> Hi, Gromacs-er:<BR>><BR>> I am curious whether the differnt water model can give different<BR>> dynamic properties, especially viscosity? In particular, which is <BR>> better<BR>> in terms of providing good viscosity - flexible water or rigid water?<BR>><BR>> In addition, what is the major advanges of using flexible water<BR>> rather than rigid water molecules? (rigid one is easier to implement,<BR>> right?)<BR>><BR>> Is there a flexible SPC/E water model? If there is, how to include<BR>> it in the Gromacs simulation?<BR>><BR><BR>Water is difficult, and I do not claim to be a world-leading authority <BR>on the subject - let's see if other people fill in :-)<BR><BR>Some comments, though:<BR><BR>1. Normally, bond constraints are good since they are a much
better <BR>approximation of the quantum mechanical ground state than a classical <BR>harmonic oscillator (flexible bond).<BR>2. Water is a bit special, partly because we also keep the angle fixed, <BR>but also because flexible bonds can help give the molecule <BR>polarizability.<BR>3. Models are usually parameterized for a specific case: either <BR>flexible or fixed. While you might improve one of the properties by <BR>using the other setup, the overall properties can often be worse.<BR>4. It is almost impossible to minimize energy efficiently with fixed <BR>waters.<BR>5. You can just add defines = -DFLEX_SPC to get the flexible versions <BR>of SPC or SPC/E, but it is mainly intented for energy minimization.<BR>6. You might need to use a smaller timestep (1fs) with flexible waters.<BR><BR>Cheers,<BR><BR>Erik<BR><BR>_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't
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