<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 9/04/2012 4:18 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopzNzaZGL9eCaDyQ6nrFFbKtKM9jrpDeT7Jw6qFkH6t0GQ@mail.gmail.com"
type="cite">By the way I've completed equilibration phase of my
system ( receptor in Ccl4-water membrane mimicking layer) in the
hight temperature conditions. :)<br>
<br>
During 3ns I gradually increased temperature from 300 to 700k with
posres applied on the Ccl4 C atoms and all atoms of protein. After
this I've changed posres applied on the protein to the backbone
atoms only and started gradually decrease fc falue ( from 1000 to
250 ). The overal system was stabile and I've noticed linnear
increase of the total energy accompanied by such increase of
temperature.<br>
<br>
Than When I've removed posres from side-chains I've noticed
bigger RMSD in potential energy of my system.<br>
<br>
The only artifact that I've noticed is that some water was moved
into the Ccl4 layer during this equilibration. How I could prevent
such layer mixing without applying posres on water?</blockquote>
<br>
I doubt you can. 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.<br>
<br>
<blockquote
cite="mid:CAALQopzNzaZGL9eCaDyQ6nrFFbKtKM9jrpDeT7Jw6qFkH6t0GQ@mail.gmail.com"
type="cite"> I need free-water in my system because I want to see
how some water move into the receptor that have a chanell wich
some internal- water cavities having functional meaning.<br>
</blockquote>
<br>
That doesn't stop you restraining water during equilibration.<br>
<br>
<blockquote
cite="mid:CAALQopzNzaZGL9eCaDyQ6nrFFbKtKM9jrpDeT7Jw6qFkH6t0GQ@mail.gmail.com"
type="cite">
Does some operation with the COM option could prevent mixing of
some differen solvent layers ?<br>
</blockquote>
<br>
Doing anything to COM of any group of many molecules is not going to
prevent one molecule from diffusing across a boundary.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopzNzaZGL9eCaDyQ6nrFFbKtKM9jrpDeT7Jw6qFkH6t0GQ@mail.gmail.com"
type="cite">At the curent moment I've difined COM as<br>
<br>
Protein_CCl4 SOL_NA_CL_XW<br>
<br>
where XW is the water observed in the X-ray structure of that
protein ( I've defined that mollecules in separate layer)<br>
<br>
Thanks for help<br>
<br>
James<br>
<br>
<br>
<div class="gmail_quote">4 апреля 2012 г. 18:14 пользователь
Justin A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
написал:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Justin,<br>
<br>
<br>
1) I've defined 5 steps for specified definition of the
time of each step as well as for more flexibile controle
of the such annealing: e.g I want that equilibration step
corresponded to the temperature between 320 and 330K will
be longer than between first step corresponded to 300-310K
etc<br>
<br>
</blockquote>
<br>
</div>
OK, that makes sense. What you showed before does not do
that, hence my confusion.
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
2) About velosities. As I understood for annealing
equilibration gen_temp must be equal to the starting
temperature of such equilibration ( gen_temp= 300 in the
above example). But in what exactly circumstances the
changing in gen_temp could be usefull? As I've told after
such annealing equilibration I want to simulate my system
on the high temperature condition for efficient
conformation sampling. Might it be that initial high
velocities could be usefull for such sampling efficacy?<br>
<br>
</blockquote>
<br>
</div>
I'm not clear on what you're asking. If you are generating
velocities (which you wouldn't after you reach your target via
SA or equilibration), then you don't need gen_temp or gen_vel.
If you're starting a new run, then gen_temp should be equal
to the ref_t value you wish to use for the simulation. If
your gen_temp and ref_t values are not the same, then it is
quite possible that the simulation will crash or give very
unexpected results due to potential instabilities in the
thermostat algorithm.
<div class="HOEnZb">
<div class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use
the www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div>
</div>
</blockquote>
</div>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>