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Ok, David, but for generate my box i do:<br>
1- editconf -f p.gro -o p.gro -bt cubic -c -d 0.7<br>
2- genbox -cp p.gro -cs spc216.gro -o p.gro -p p.top<br>
my peptides have diferent structure , and then my BOX <br>
and my number of H2O are diferent, my question is.<br>
hOW COULD I GENERATE exactly the same number of solvent <br>
molecules and box size.<br>
thanks<br>
<br>
<br>
<br>
David wrote:<br>
<blockquote type="cite"
cite="mid1059593038.1744.13.camel@h28n2fls34o1123.telia.com">
<pre wrap="">On Wed, 2003-07-30 at 23:43, Osmany Guirola Cruz wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Thanks again Xavier,
I have this problem:
I have a peptide whit unknown structure, whit "modeler" i get 10
diferents structures of my peptide, and then.....
i use SA whith the ten models to obtain a "superminimized structure"
but my final structures are NOT similar
:-( . i have the idea that my simulations converge to a unique
structure (my SA = "1000K" to 300K) you say 10 000 i will probe
with 10000 to see what happens. ???????
</pre>
</blockquote>
<pre wrap=""><!---->I wouldn't use SA in this case, but rather simulated the peptides in
solvent (each of the ten with exactly the same number of solvent
molecules and box size) and then first let it relax and then do a short
free simulation to measure the energy (Epot including solvent). Your
lowest energy is the most likely structure, although the forcefield can
be wrong.
</pre>
<blockquote type="cite">
<pre wrap="">
Xavier Periole wrote:
</pre>
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<pre wrap="">
I guess you have been reading papers from NMR procedures to
generate their models corresponding to the data. If that what you
are doing It would be easier to get a program that NMR people
use, is is probably implemented
It seeems difficult to do that automatically in gromacs, at least
for me.
I guess you that could modify the strength of the constant on the
angles
and bonds in the parameter file and do that for each temperature you
need but that's gonna to be a pain in the ...
I don't know what you are doing but I can assure you that at 10000 K
the system is pretty flexible. Try to simulate it for 10 ps at 10000
K
and look at the trajectory !! It should convice you. But I don't
know if
it is relevant for your problem.
XAvier
</pre>
</blockquote>
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