<div>Dear chris</div>
<div>Thanks for your reply</div>
<div> </div>
<div>1-I am not sure,Since we need the know the variations of free energy along a specific degree of freedom of system(for example z axis),so the springs must be 1 dimensional to allow drug to oscilate only in one dimension(z axis).</div>
<div>Let me say my question in other words:</div>
<div>Do we need to do sampling just in phase space related to z axis(1 dimensional) or we can do sampling in other places(if it be 3 dimensional),Although we still want the variation of free energy along z axis?</div>
<div> </div>
<div>2-evry windows have a width(for example 0.02 nm),Besides according to Hock's law knowing the oscilation amplitude is possible when you have the K and the mass and total energy:1/2 k(x/2)^2=1/2 m v(max)^2</div>
<div> </div>
<div>3-my question in other words:</div>
<div>Since we need overlapping the distribution densities of each windows,Does the drug need to enter to the neighbour windows a little ? <br></div>
<div>Thanks in advance for your reply<br></div>
<div class="gmail_quote">On Tue, Mar 15, 2011 at 9:54 AM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">1. Depends on how you set them in your .mdp file. It could be either.<br><br>2. There is no general method. Use trial and error. Also, your question is flawed, K defines X. Unless by "length of one windows" you meant the distance between neighbouring centers of restraint (umbrellas).<br>
<br>3. you need overlapping distributions. Let's leave it at that. I have not seen any general treatment of what K is required and I am rather sure that it is impossible to predetermine the necessary force constants (K) unless you know the PMF. If you need to know the PMF beforehand then this is not a general solution and also probably useless since the whole purpose is to get the PMF.<br>
<br>Chris.<br><br>-- original message --<br><br>Dear All<br>afew question in umberella sampling tutorial:<br>1-We do umberella sampling for each of 25 simulation windows,while using a<br>spring(harmonic potential),Are these springs 1 or 3 dimensional?<br>
<br>2-Suppose the length of one windows is X nm,what is the approperiate K<br>(spring constant) for this window?Is there a general way to determine this<br>value?<br><br>3-I think the K must be such that the oscilation amplitude be a few larger<br>
than X/2, because we need overlapping of density distribution for analysing<br>with wham method, am I right?<br><br>Thanks in advance<br><font color="#888888"><br><br><br>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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