<div>Thanks for clearing the doubt.</div>
<div> </div>
<div>Is that more easier to get equlibrium to use unchanged mass when doing LJ turning on/off?</div>
<div>I ask this since I found the forwards and backwards mutation free energy are more consistant if I do not change the mass. Accidentally?</div>
<div> </div>
<div>LQ<br><br></div>
<div class="gmail_quote">On Thu, Jun 19, 2008 at 4:26 AM, David Mobley <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">You can change the mass if you like. Basically, the net free energy<br>change associated with changing the mass should end up being zero so<br>
it will be irrelevant. The mass of course affects the dynamics and<br>things like the velocities, but based on equipartition you can<br>convince yourself that the free energy change will be zero.<br><br>David<br>
<div>
<div></div>
<div class="Wj3C7c"><br>On Fri, Jun 13, 2008 at 12:04 AM, friendli <<a href="mailto:friendli2000@gmail.com">friendli2000@gmail.com</a>> wrote:<br>> Dear all,<br>><br>> I am calculating FE using TI. I have a question about mutating existing<br>
> atoms with different mass.<br>> for example, using ffG53a6 force field, in one case i need to mutate CH2 to<br>> CH3,<br>> should I use<br>> [ atoms ]<br>> 17 CH3 2 ALA CB 6 0 15.035 CH2 0<br>
> 14.027; qtot 1<br>><br>> OR<br>><br>> 17 CH3 2 ALA CB 6 0 15.035 CH2 0<br>> 15.035; qtot 1<br>><br>> I notice from Prof. Alan Mark's online FE course, he mutates a H atom to a O<br>
> atom, but does not change its mass.<br>> The line is :<br>> 12 HC 1 PHE HZ 6 0.1 1.008<br>> OA -0.548 1 1.008<br>><br>> Can somebody explain a bit why we should not change the mass accordingly?<br>
><br>><br>> thank you<br>><br>> LQ<br>><br>> I though I sent this email but why I can not see it. There may be something<br>> wrong with my email software. so I send here again. sorry<br></div></div>
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