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<pre wrap=""><span class="moz-txt-citetags">>></span>/ Thank you.
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<pre wrap=""><span class="moz-txt-citetags">> </span>/>/ But i have one last question:
<span class="moz-txt-citetags">> </span>/>/For epsilon_rf i use the relative permittivity of the medium. I simulate
<span class="moz-txt-citetags">></span>in
<span class="moz-txt-citetags">> </span>/>/vacuum so epsilon_rf would be 1?
<span class="moz-txt-citetags">> </span>/GROMOS ff is not parameterized for vaccum simulations of the b-something
<span class="moz-txt-citetags">> </span>version ... have look at the paper.
<span class="moz-txt-citetags">></span>
<span class="moz-txt-citetags">></span>
<span class="moz-txt-citetags">> </span>So i should use ffG43b1 instead of the other GROMOS96 force fields?
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<pre wrap=""><!---->That would be the right choice for the GROMOS43 ff series.
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<pre wrap=""><span class="moz-txt-citetags">> </span>In the GROMACS manual i found that the cut-off-distance must at least be 1.4
<span class="moz-txt-citetags">></span>nm for the GROMOS96 force field.
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<pre wrap=""><!---->Never believe what is written in a manual :))
It is always better to keep the values that are used for parameterization
(the one I gave you) when using a force field. The idea that bigger = better
does not work ... you change the balance of forces and thus the properties
of the force field.
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<pre wrap=""><span class="moz-txt-citetags">> </span>So can i use: type = cut-off; rlist = 1.4 and r_x = 1.7?
<span class="moz-txt-citetags">> </span>(the problem is that the only reference i find for ffG43b1 is the GROMOS
<span class="moz-txt-citetags">></span>manual, and that's not free avaible)
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<pre wrap=""><!---->Any paper from van Gunsteren group or Alan Mark groujp (GROMOS developers)
would describe the simulation setup: no need of the manual for this.
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<pre wrap=""><span class="moz-txt-citetags">> </span>Thanks for an answer
<span class="moz-txt-citetags">> </span>Thomas
<span class="moz-txt-citetags">></span>
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I looked in some older papers but found no values for epsilon_r and
_rf. From older posts of this mailing list I got the impression that
epsilon_r = 1 and epsilon_rf the value of the relative permitivity of
the medium. In the case of a simulation in vacuum epsilon_rf would be
also 1 and then I have no correction from the reaction field, also
grompp tells me that epsilon_r = epsilon_rf would be meaningless with a
reaction field. So I'm puzzeld.<br>
If both epsilon values have the same value, is it then equal to normal
cut-offs (type = cut-off)?<br>
Sorry for the many questions.<br>
Thomas<br>
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