Hi Mark<div>Thanks.<br><div>I created a box of 6x6x6 inserting 7 molecule of chaps with genbox.Then I solvated this box with genbox using -maxsol 500 and spc216.gro. On visualization, at this stage itself uniform solvation did not occur and I got water in one region and chaps molecule spread throughout box but not inside water. I should have visualized it earlier before going for minimization. Please help me.</div>
<div>shahid Nayeem <br><br><div class="gmail_quote">On Thu, Jan 27, 2011 at 11:36 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"><br><br><span>On 01/27/11, <b>shahid nayeem </b> <<a href="mailto:msnayeem@gmail.com" target="_blank">msnayeem@gmail.com</a>> wrote:</span><blockquote style="border-left:1px solid rgb(0, 0, 255);padding-left:13px;margin-left:0pt" type="cite">
<div>Dear All<div>I am trying to prepare a solvation box of chaps. After generating .itp and .gro at ProDrg and thorough check of charges, I started with a box size of 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I get a box where all water molecules get accumulated in two three small region within the box and all chaps molecules gets accumulated in another small regions.I wanted near random uniform distribution of chaps in water. Any help from user, where I am wrong and what should I do.</div>
</div></blockquote><blockquote style="border-left:1px solid rgb(0, 0, 255);padding-left:13px;margin-left:0pt" type="cite"></blockquote><br></div>You haven't told us how you've solvated the system (e.g. with genbox), that it looked OK when you visualized it between each step, and that you're sure your observations cannot be rationalized as a periodicity artefact.<br>
<font color="#888888"><br>Mark
</font><br>--<br>
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