Chris, <br><br>I understand, Sorry for that . Actually I mixed up the concept of SteeredMd with umbrella sampling. So I was confused whenever you people gave suggestions. <br><br>Now I thing I got the idea , Thanks for you people. I will try myself and see. Thanks once again. <br>
<br>-Aswathy<br><br><div class="gmail_quote">On Tue, May 11, 2010 at 6:48 PM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
It represents a difference in coordinate space. You'll get the most out of this list if you continue to try to solve your problems before posting and avoid submitting every question/problem that you hit upon under a continuously in-use title. Did you try it and look at you -px output file? I suggest that you do some tutorials. Also, set up a test system and pull two water molecules apart within a box of water and use VMD to see what happens. Then try a slightly more difficult test system... these are the types of things that worked for me.<br>
<br>
pull_init1 = 0 0 -5<br>
pull_init1 = 0 0 -4.9<br>
pull_init1 = 0 0 -4.8<br>
...<br>
pull_init1 = 0 0 4.9<br>
pull_init1 = 0 0 5<br>
<br>
But it's up to you to determine the spacing. You need to get good overlap in order to be able to do WHAM. If you don't know how to figure that out then it's time for some reading.<br>
<br>
Good luck,<br>
Chris.<br>
<br>
-- original message --<br>
<br>
Hi Chris,<br>
<br>
Thank you very much for your detailed mail.<br>
<br>
Now I have a doubt on this pull_init parameter. i read your previous posts<br>
regarding this, but still have a confusion.<br>
<br>
My query is that for each configuration when I run umbrella sampling, will<br>
this pull_init value needs to change?(I suppose so, if its true how?)<br>
<br>
When it should be negative and positive?<br>
<br>
<br>
Could you please explain this. Thanks for your valuable time<br>
<br>
Thanks & Regards,<br>
Aswathy<br>
<br>
<br>
On Mon, May 10, 2010 at 9:55 PM, Chris Neale <<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</a>>wrote:<br>
<br>
[Hide Quoted Text]<br>
Pick a small collection of backbone atoms near the center of your channel<br>
and use them as your reference group. Overcome the sign problem by optimal<br>
selection of pull options (see below). pull_pbcatom values should not be<br>
important<br>
if you select your groups as I suggest -- otherwise be sure to understand<br>
how they work.<br>
<br>
<br>
; COM PULLING<br>
pull = umbrella<br>
pull_geometry = position<br>
pull_dim = N N Y<br>
pull_start = no<br>
pull_nstxout = 250<br>
pull_nstfout = 250<br>
pull_ngroups = 1<br>
pull_group0 = MY_SELECTION_OF_BACKBONE_ATOMS<br>
pull_pbcatom0 = 0<br>
pull_group1 = LIGAND<br>
pull_pbcatom1 = 0<br>
pull_init1 = 0 0 THISDIST<br>
pull_rate1 = 0<br>
pull_k1 = 500.0<br>
pull_vec1 = 0 0 0<br>
<br>
Chris.<br>
<br>
-- original message --<br>
<br>
I think Justin meant that you have various positions of the ligand in the<br>
channel (from the SMD), so you don't need to make a new run to determine new<br>
positions in the channel. You need only new umbrella sampling simulations.<br>
<br>
Yep, the movement of the particle will also matter, because if the particle<br>
moves much on the z-axis, the distance between the particle and the ligand<br>
will change. So you would want the particle fixed relative to the channel.<br>
Two ideas:<br>
Place the particle above the entrance of the channel. Pick three atoms from<br>
the entrance of the channel and determine the distance between the atoms and<br>
the particle. Then use distance_restraints or constraints with a<br>
'bondlength' equal to the measured distance. If everything goes right the<br>
particle would stay where you placed it, since it does not interact with the<br>
enviroment it should not really influence your simulation (only through the<br>
constraints or distance_restraints).<br>
I don't now how big your system is, but it would probably be a good idea to<br>
make a short test simulation, to look if the particle changes the system<br>
behavior.<br>
But it's only an idea, i hope other people comment it.<br>
<br>
Greetings<br>
Thomas<br><font color="#888888">
<br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Aswathy<br>