<br><br><div class="gmail_quote">On Thu, May 17, 2012 at 5:48 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</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"><br>
<br>
On 5/17/12 11:50 AM, Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
My tube is finite. I increased my box so the water could interact with all water<br>
molecules. The same problem: My minim.mdp<br>
<br>
; minim.mdp - used as input into grompp to generate em.tpr<br>
; Parameters describing what to do, when to stop and what to save<br>
integrator = steep ; Algorithm (steep = steepest descent minimization)<br>
emtol = 10.0 ;<br>
emstep = 0.001<br>
nsteps = 50000 ; Maximum number of (minimization) steps to perform<br>
nstxout = 1<br>
; Parameters describing how to find the neighbors of each atom and how to<br>
calculate the interactions<br>
nstlist = 1 ; Frequency to update the neighbor list and long range forces<br>
ns_type = grid ; Method to determine neighbor list (simple, grid)<br>
rlist = 1.4 ; Cut-off for making neighbor list (short range forces)<br>
coulombtype = PME ; Treatment of long range electrostatic interactions<br>
rcoulomb = 1.4 ; Short-range electrostatic cut-off<br>
rvdw = 1.4 ; Short-range Van der Waals cut-off<br>
pbc = xyz ; Periodic Boundary Conditions (yes/no)<br>
<br>
Well... no clue...<br>
<br>
</blockquote>
<br></div>
Then the diagnostic tips I listed before still apply, as well as those listed on the webpage linked from what I posted earlier.<div class="HOEnZb"><div class="h5"><br>
<br>
-Justin<br></div></div></blockquote><div><br>Thank you Jusin! By the way, how can I create infinite tube in gmx? <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="HOEnZb"><div class="h5">
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
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