<div dir="ltr"><div>Hi,</div>
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<div>i'm simulating a surface in water and ions which is composed of 6X6 Carbon atoms arranged on a 2-d lattice. (using ffamber99)</div>
<div>i want to keep the spacing between C-C neighbouring atoms at 0.34 Angstrom (or some other spacing of choice..), and to maintain the surface rigid and planar</div>
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<div>for that i added to the [ bonds ] section at the topology file c0 values and force constants as following:</div>
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<div>[ bonds ]<br>; ai aj funct c0 c1 c2 c3<br> 1 2 1 3.400000e-01 3.744680e+05<br> 1 7 1 3.400000e-01 3.744680e+05<br> 2 3 1 3.400000e-01 3.744680e+05<br>
..</div>
<div>and so on..</div>
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<div>and similarly added 90 and 180 degrees bond angle constrains between triads of atoms in the surface according to their location.</div>
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<div>the thing is , i'm affraid my constraint of c0 of 3.4 Angst. is in some conflict with the definition of C-C bond length which is defined somewhere in the amber files (if i'm turning the constraint on co off the atoms approach each other and the spacing is lost)</div>
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<div>my questions are:</div>
<div>a) do you think i should define a new dummy atom? and in which files should it be done? - i'm asking because i didn't find a clear answer in the manual</div>
<div>b) is there any other bond function (what number?) which may ignore the definition of the C-C length and treat only the c0 constraint?</div>
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<div>if someone can answer or guide me to relevant sections in the manual i'll be most thankful!</div>
<div>amir</div>
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