<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
--></style>
</head>
<body class='hmmessage'>
<br><br>> Date: Tue, 1 Dec 2009 07:44:51 +1100<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Tabulated potentials make newbies crazy<br>> <br>> ms wrote:<br>> > Mark Abraham ha scritto:<br>> > > Sorry, I was a bit incomplete last night. Charge groups are the<br>> >> fundamental unit for neighbour-searching (3.4.2) to construct lists of<br>> >> charge groups for nonbonded interactions, which determine lists of<br>> >> atom-atom interactions. However, the nonbonded interactions are<br>> >> evaluated as nested sums, first over energy groups. So for energy groups<br>> >> of Protein and SOL, the neighbour search finds all pairs of charge<br>> >> groups that are both Protein and inside the cutoffs, and lists them.<br>> >> Then all Protein-SOL similarly, then all SOL-SOL. This requires that the<br>> >> energy groups be a union of only complete charge groups (and I am not<br>> >> aware that this is spelled out anywhere in the manual!). So for energy<br>> >> groups of Calpha, Rest_of_Protein and SOL, it would be necessary to use<br>> >> an individual charge group for each Calpha. This would usually mean it<br>> >> has a net non-integral charge that is equal in magnitude of the charge<br>> >> of the group from which it is taken. It is well known that small charge<br>> >> groups of non-integral charge can then wander back and forth across<br>> >> cut-off boundaries and generate artefacts.<br>> > <br>> > Ok, thanks for the clarification. This doesn't suggest a trivial<br>> > solution to the problem, quite the opposite: I understood correctly that<br>> > charge groups must be neutral, and this is impossible to do if we put<br>> > each C-alpha as a charge group.<br>> > <br>> > I can coarse the thing further -that's quite the plan, actually- and<br>> > eliminate electrostatics, but I hoped to have a look at what happens<br>> > with the new potential and getting it right, before going so far.<br>> > <br>> > So, even if the following:<br>> >>> The problem is that since I have a single molecule now, and the single<br>> >>> molecule must be neutral, so it must be all a single charge group<br>> >>> ("Therefore we have to keep groups of atoms with total charge 0<br>> >>> together. These groups are called charge groups.", 4.6.2).<br>> > <br>> > is not entirely correct, it is indeed correct that charge groups<br>> > *should* be neutral. Isn't it?<br>> <br>> Indeed. See 3.4.2 and ref therein.<br>> <br><br>Charge groups do not have to be neutral at all.<br>If you use plain cut-off's or a reaction field without buffer, neutral charge<br>groups will help a lot to reduce cut-off artifacts.<br>However with PME or reaction-field-zero (with a buffer) the charge of<br>a charge group does not matter at all.<br>We should add a few lines to the manual explaining this.<br><br>Berk<br><br>> >> If you're running in single precision, that precision cannot represent<br>> >> values as large as 10^41. Since in any simulation (but particularly<br>> >> coarse-grained one) non-bonded atoms aren't going to get this close, the<br>> >> values are next to irrelevant. Just choose 10^38 for anything larger<br>> >> than that.<br>> > <br>> > Right, it is probably precision problem. Thanks.<br>> > <br>> >>>>> Now, my questions are:<br>> >>>>> - What is the accepted range of values in tables?<br>> >>>> I don't think this is the problem.<br>> >>> It is the least problem probably, given my confusion on energy-charge<br>> >>> groups, but it seems it is too...<br>> >>><br>> >>>>> - How do I define a steep repulsion potential correctly?<br>> >>>> It's terse, but manual 6.7 seems to have the necessary information.<br>> >>> 6.7 is one of the references I am obviously using, but it gives only<br>> >>> general (even if essential!!) information, nothing speficic on "good" or<br>> >>> "bad" potential shapes/values. But probably that's the least problem :)<br>> >> Knowing a sensible shape is your problem, if you're choosing to<br>> >> unbalance the force field by changing one of the contributing potentials...<br>> > <br>> > I meant "sensible" in the meaning of "can be interpolated more or less<br>> > faithfully / will be calculated with more or less artefacts" -of course<br>> > if it makes sense in the model is my problem...<br>> <br>> The cubic spline interpolation will do a mighty fine job of any function <br>> that is suitably continuous provided that the density of points is <br>> sufficiently fine... interpolating a sinusoid with a density comparable <br>> with the period would obviously be a disaster!<br>> <br>> Mark<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
</html>