<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 28/03/2012 10:48 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopyxgvufp80mHUQhpWiWYR4yZrPF4+f=x_5tp575k+QEQg@mail.gmail.com"
type="cite">Mark,<br>
<br>
This sounds like I use very small forces but expect reasonable
effect. But I've applied different forces with step-by-step
increasing of force constants ( from very softest comparable with
the thermal motion ( 0.1 kj mol nm-2) to relatively hight (10).
As the consequence I've observed effect of application of that
harmonic constraints wich I've defined in the r0 and r1 range but
in some case ( where forses were were hight I've seen perturbation
of my structures) and when constraints were low ( in accordance to
my literature) I've not seen desired effect like the selection of
the constraints was wrong ( but actually all restraints were
applied on the correct possitions). This was seen by measurement
of the distances between atom pairs wich were contrained. Eg If I
define this distances in the 0.1<Rij<0.4 ( r0=0,1 r1=0,4 for
this instance) range the real distance between i and j atoms in
the simulated structure was lower or higher of the defined range.
<br>
</blockquote>
<br>
What's reasonable depends on the objective. If you want to keep
something very close to where it *already* is, and it's reasonably
happy there already, then you don't generally need much in the way
of restraints. If your starting configurations are different from
what you wish to achieve, then you're going to have to
metaphorically speak loud enough to be heard over the thermal
commotion, and then loud enough to cross the relevant barriers. That
can mean big restraint forces and tiny integration steps and lots of
tweaking and praying. Or finding a new starting configuration that's
more relevant for the objective.<br>
<br>
For comparison, pdb2gmx generations position restraints with 1000 kJ
mol nm-2 force constants for helping people not perturb their
structures during equilibration. Your distance deviations are much
larger than will usually occur with PR, so you don't want to go that
large.<br>
<br>
<blockquote
cite="mid:CAALQopyxgvufp80mHUQhpWiWYR4yZrPF4+f=x_5tp575k+QEQg@mail.gmail.com"
type="cite">
<br>
By the way I've found that besides such harmonic restraining also
I can apply more rigid holo restraints from specified value. Could
you tell me where I could find information of the application of
such restraints in the topology of my protein? As I understood
this could be done by means of editing of the bond enty in
topology but what exactly specified type should I applied on the
restried atoms?<br>
</blockquote>
<br>
Rigid constraints are not useful for you, because your initital
conditions are a long way from your target conditions. Any kind of
harmonic potential has the same or worse issues than you already
have.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopyxgvufp80mHUQhpWiWYR4yZrPF4+f=x_5tp575k+QEQg@mail.gmail.com"
type="cite">
<br>
<br>
Thank for help again,<br>
<br>
James<br>
<br>
<div class="gmail_quote">22 марта 2012 г. 17:32 пользователь Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
написал:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">If
there's a car at the bottom of one valley in the Alps, and you
think it should be two valleys over, and you pull it with a
trained cat... it's not going to move much. How big an animal
you need depends on the geography. There need not even be a
reasonable route for you to take, if the target valley is
effectively on Mars.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span>
<div class="HOEnZb">
<div class="h5"><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>