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On 25/10/2011 3:30 AM, James Starlight wrote:
<blockquote
cite="mid:CAALQopzz50Uc+WvTtNMn2eZyVyyBgGDmQGdTeLKMwz5xk1XT2A@mail.gmail.com"
type="cite">I understand this but I've not been able found such
information. I dont need in the most accurately parametries for
all cutt-offs of my system but I want to gain inside into the
basic cutt- offs worked with the Normal mode analysis.<br>
</blockquote>
<br>
The cut-offs are particular to the force field, not the manner in
which the force field is used (EM vs MD vs whatever). There are
literature references in the GROMACS manual, and also in the
published work that you have been reading because it has objectives
similar to yours. (hint, hint) <br>
<br>
<blockquote
cite="mid:CAALQopzz50Uc+WvTtNMn2eZyVyyBgGDmQGdTeLKMwz5xk1XT2A@mail.gmail.com"
type="cite">
<br>
E.g I've found that PME is not worked here. </blockquote>
<br>
PME does work here. Last time you were apparently mis-matching
files...<br>
<br>
<blockquote
cite="mid:CAALQopzz50Uc+WvTtNMn2eZyVyyBgGDmQGdTeLKMwz5xk1XT2A@mail.gmail.com"
type="cite">So I must to constrain my system with simplest
cuttoffs. Could you provide me with the simple example e.g cutt of
for interaction beetwen C-alpha atoms only etc? <br>
</blockquote>
<br>
You can't do that, and shouldn't even if you could.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopzz50Uc+WvTtNMn2eZyVyyBgGDmQGdTeLKMwz5xk1XT2A@mail.gmail.com"
type="cite"><br>
James<br>
<br>
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<div class="im"> <br>
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These are particular to the force field involved, not the
software. Please consult the appropriate literature, and see
what others have used for similar work.
<div class="im"><br>
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