<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 9/04/2012 7:27 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopzjU=4XBe2q3Dw-Pv8Lmqd2AxBPA-m_8PQ5r2812cxqog@mail.gmail.com"
type="cite">Mark,<br>
<br>
<div class="gmail_quote">
<div> </div>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">If you make your layer
boundaries perpendicular to some axis then you can use
position restraints on water oxygens that have non-zero
force constants only with respect to that axis. Then relax
the water position restraints before any others.
<div class="im"><br>
</div>
</div>
</blockquote>
<div><br>
Yes, I've thought about this to apply posres onto selected
coordinates to allow waters move only laterally relavitely
protein-membrane-like system. But this prevent to move water
into the receptor interious as well so it's not very good
aproach. <br>
</div>
</div>
</blockquote>
<br>
Assuming you're raising your temperature during equilibration and
then running at high temperature, then you don't want water moving
into the receptor interior during equilibration for the same reason
you didn't want water moving into the CCl4. And you're going to run
further equilibration after taking off all the restraints anyway,
right? And if water moves into the receptor interior, then it
probably does that under high-temperature equilibrium conditions...<br>
<br>
<blockquote
cite="mid:CAALQopzjU=4XBe2q3Dw-Pv8Lmqd2AxBPA-m_8PQ5r2812cxqog@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>
<br>
Also I've thought about vary of the ref_t oprions wich I've
defined separatelly for protein_membrane layer and for
water_ions. As I've told I want to increase confoprmation
sampling of my protein by means of gradually temperature
increasing. Could I rise only ref_t for the protein_ccl4 layer
with the apllied posres on the protetn (backbone atoms) and
ccl4 ( C atoms) during nvt equilibration while not changing
ref_t for water and ions ? Will my system be some unphysicall
in that case ? Or as the alternative way could I decrease
ref_t for the water_ions layer in the end of nvt equilibration
to allow water to move out from the Ccl4 layer?<br>
</div>
</div>
</blockquote>
<br>
Please check your spelling. Attention to detail is very important in
doing such simulations, and you don't want to create the impression
your simulation settings might look similar to the above :-) On
point, the reference temperature has little to do with whether
phases diffuse into (or out of) each other, and lots to do with what
ensemble you might be sampling. The actual temperature controls the
rate of such diffusion, of course, but if the non-bonded
interactions allow for intermixing, then you'll get some degree of
that regardless of any other setting. You'd be well advised to check
that your CCl4-water boundary behaves acceptably before you invest
in the protein simulation...<br>
<br>
Mark<br>
</body>
</html>