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On 25/01/2012 9:45 PM, Banafsheh Mehrazma wrote:
<blockquote
cite="mid:CADNrWT5L1OBe=tBxar1TsUqLKkzv38M2ehiUEyeucHX+8KuNww@mail.gmail.com"
type="cite">Hi everyone;
<div>I am about to minimize a system in 3 steps; </div>
<div>first, I want my molecule to be minimized, so I used ''define<span
class="Apple-tab-span" style="white-space:pre"> </span>=
-DPOSRES_WATER " in my *.mdp file., Then after using g_energy
command to make potential.xvg, it gave me a nice diagram. Next I
wanted to perform minimization with my protein to be constained
and then a whole_system_minimization without any constraints.
However, the next diagrams are not appropriate; one is linear,
and another is increasing, instead of decreasing!</div>
<div>I should mention that they all converged before 1340, 201, 47
steps, respectively, and I set emtol option to be 100 and nsteps
= 500000.</div>
<div>Do you know what is the problem?</div>
<br>
</blockquote>
<br>
Maybe your system is already well minimized and these relaxations
are not doing anything useful. Also, be sure to use the terminology
of constraints and restraints correctly.<br>
<br>
Mark<br>
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