Sorry, I wasn't too clear in the first message. I will be using OpenMM Gromacs, which does support implicit solvent. <div>My current energy minimization steps only lower the energy to -5E3. Is this okay considering water is not around?<br>
<div>Is is necessary to do equilibration if I am using implicit solvent? Is so, can anyone direct me to reasonable parameters?</div><div><br><div>Thanks! <br clear="all">Grace<br>
<br><br><div class="gmail_quote">On Wed, Apr 15, 2009 at 2:55 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im">Grace Tang wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello All,<br>
<br>
I am doing energy minimization on a protein crystal structure to relax it. Afterwards, I plan to run md simulation with implicit solvent. I am new at this and have many questions.<br>
1. Should the implicit solvent conditions be enabled when I run the energy minimization?<br>
</blockquote>
<br></div>
No - while GROMACS has some vestiges in the user interface of an earlier attempt to implement implicit solvation simulations, these will not functional until at least version 4.1.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
2. What minimum potential energy should I expect (i know that when explicit water is present, the energy often reaches -10E5 or -10E6)<br>
</blockquote>
<br></div>
Negative, and vaguely proportional to the number of atoms.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
3. What kind of emtol is appropriate? Is it better to set it high so that the system converges, or is it okay if machine precision is reached. <br>
</blockquote>
<br></div>
It's pretty much irrelevant for preparing a system for MD. You'll have to equilibrate it later, and the value of an EM step is merely relieving any bad atom-atom contacts before they turn into huge accelerations. If the equilibration doesn't crash, you did enough EM.<br>
<br>
Mark<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Below are 2 example runs I did with implicit_solvent = no<br>
When I decreased the step size, the system did not converge anymore. I was wondering if this was due to chance, precision issues (I am using single precision), or perhaps the emstep = 0.1 was reaching a nearby minimum and 0.01 was reaching the local minimum. Note, maximum force gets rather large when convergence is to machine precision.<br>
<br>
emtol = 1000<br>
emstep = 0.1<br>
Steepest Descents converged to Fmax < 1000 in 29 steps<br>
Potential Energy = -4.9613008e+003<br>
Maximum force = 6.4596338e+002 on atom 235<br>
Norm of force = 1.0625026e+002<br>
<br>
emtol = 1000<br>
emstep = 0.01<br>
Steepest Descents converged to machine precision in 25 steps,<br>
but did not reach the requested Fmax < 1000.<br>
Potential Energy = -3.9642480e+003<br>
Maximum force = 5.1200122e+003 on atom 416<br>
Norm of force = 3.6602789e+002<br>
<br>
Any advice is greatly appreciated. Much thanks!<br>
- Grace<br>
<br>
<br></div>
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