I still want to suggest that segmentation fault doesn't occur due to large no. of insertion molecules the reason being that i, once tried to insert only 1 molecule and it came up with seg. fault again . I am very sure that i have space for atleast some(>1) no. of water molecules.<div>
<br></div><div>Amit<br><br><div class="gmail_quote">On Sun, Sep 20, 2009 at 6:38 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">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>
Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi everyone,<br>
<br>
I have been trying to insert a fixed no. of water molecules in my system. I first tried the -cp -cs options and could insert some water molecules. But I still need to insert few more water molecules and for that i tried using the -nmol -ci option. I made a file named "insert.gro" which has a single water molecule with the right volume associated with it. But this option gave a segmentation fault and i am not sure why its doing that? May be there's not enough space for additional water but it should not give a segmentation fault for that reason. Is there something wrong with my idea?<br>
<br>
</blockquote>
<br></div>
A segmentation fault with this approach generally indicates that the requested number of inserted molecules will not fit.<br>
<br>
Alternately, you can try -cs spc216.gro -maxsol (your number)<br>
<br>
If the second approach also fails, I would think that would be strong evidence that what you're trying to do won't work.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
The insert.gro looks like the following<br>
<br>
H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=0.31034NM,WFVG,MAR. 1984<br>
3<br>
1SOL OW 1 .130 .128 .113<br>
1SOL HW1 2 .037 .126 .150<br>
1SOL HW2 3 .131 .089 .021<br>
0.31034 0.31034 0.31034<br>
<br>
I also tried various other box (larger) sizes for this but it didnt help. <br>
Thank you in advance.<br>
<br>
Amit<br>
<br>
<br></div>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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