<div style="font-family: 'Times New Roman'; font-size: 16px;"><br /><br /><span>On 09/21/09, <b class="name">xiao shijun </b> <xshijun@gmail.com> wrote:</span><blockquote cite="mid:432e5af80909202238g109fa3cdj7912048d3401772b@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"> Mark wrote:<br /> > xiao shijun wrote:<br /><div style="margin-left: 40px;">
>> Hi everyone,<br />
>> Recently, I met a problem on the force-field. I am doing something<br />
>> on the calcium carbonate, and want to simulation it with gromacs.<br />
>> The shell model for oxygen has been emploied in my system. When I<br />
>> considered the non-boned potential associated with interactions between<br />
>> atoms<br />
>> in the same CO3 group, I only need to take O-O buckingham interaction<br />
>> into account, but any electric interaction. How could I realize that in<br />
>> my .top file.<br />
>> First, I tried to use [pairs] to eliminate electric interaction, but<br />
>> I can't add the buckingham interaction of O-O because there is no<br />
>> buckingham<br />
>> options for LJC14. I want to know if anyone of you have such the<br />
>> experience. Thanks!!<br /></div>
<br /> >Usually you would not define a nonbonded interaction for atoms that are<br /> >so close together, since their interaction should be able to be modelled<br /> >adequately with the C-O bond and O-C-O angle (and perhaps with CHARMM,<br />
>an interaction harmonic the O-O distance as a Urey-Bradley term).<br /> <br /> Thanks for Mark's suggestion. But I want to reproduce the simulation from the other paper,<br /> The paper describe the force-field that O-O nonbonded interaction in the same carbonate should be considered.<br />
In addition to that, I can't use buckingham potential in [pairs], even choose funct = 2. I am wondering<br /> if I want to describe 1-4 interaction by Buckingham, what could I do? </div></blockquote>This is one application for setting nrexcl for moleculetypes. You don't want exclusions for particles 2 bonds apart, so set this to one. See chapter 5.<br _moz_dirty="" /><br _moz_dirty="" />If that doesn't work, then if the "bonded" interactions are merely harmonic distance potentials, then GROMACS permits a form of them that doesn't create a bond (bond type 6, IIRC, check chapter 5; or constraint type 2). Thus, the automated exclusion mechanism won't be involved, and you can have Buckingham O-O so long as you have Buckingham for all other LJ interactions. You will need manual exclusions for C-O pairs, I guess. Thus<br _moz_dirty="" /><br _moz_dirty="" />[ atomtypes ]<br _moz_dirty="" />C #nonbonded parameters go here<br _moz_dirty="" /><div _moz_dirty="" class="mimepart text html">O #nonbonded parameters go here<br _moz_dirty="" /><br _moz_dirty="" />[moleculetype]<br _moz_dirty="" />carbonate<br _moz_dirty="" /><br _moz_dirty="" />[atoms]<br _moz_dirty="" />C<br _moz_dirty="" />O1<br _moz_dirty="" />O2<br _moz_dirty="" />O3<br _moz_dirty="" /><br _moz_dirty="" />[bonds]<br _moz_dirty="" />C-O1 # type 6<br _moz_dirty="" />C-O2 # type 6<br _moz_dirty="" />C-O3 # type 6<br _moz_dirty="" /><br _moz_dirty="" />[exclusions]<br _moz_dirty="" />1 2<br _moz_dirty="" />1 3<br _moz_dirty="" />1 4<br _moz_dirty="" /><br _moz_dirty="" />Whether this works may depend on whatever else is in your system, though.<br _moz_dirty="" /><br _moz_dirty="" />Mark<br />
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