yes you are right its a bug, everything works well on the most recent version.<div><br></div><div>Thank you<br><br><div class="gmail_quote">On Sun, Sep 20, 2009 at 6:55 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">
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.<br>
<br>
</blockquote>
<br></div>
Which version of Gromacs are you using? There was a bug in genbox 4.0.3, but was fixed prior to 4.0.4.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Amit<div><div></div><div class="h5"><br>
<br>
On Sun, Sep 20, 2009 at 6:38 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Amit Choubey wrote:<br>
<br>
Hi everyone,<br>
<br>
I have been trying to insert a fixed no. of water molecules in<br>
my system. I first tried the -cp -cs options and could insert<br>
some water molecules. But I still need to insert few more water<br>
molecules and for that i tried using the -nmol -ci option. I<br>
made a file named "insert.gro" which has a single water molecule<br>
with the right volume associated with it. But this option gave a<br>
segmentation fault and i am not sure why its doing that? May be<br>
there's not enough space for additional water but it should not<br>
give a segmentation fault for that reason. Is there something<br>
wrong with my idea?<br>
<br>
<br>
A segmentation fault with this approach generally indicates that the<br>
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<br>
strong evidence that what you're trying to do won't work.<br>
<br>
-Justin<br>
<br>
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<br>
didnt help.<br>
Thank you in advance.<br>
<br>
Amit<br>
<br>
<br>
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Virginia Tech<br>
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<br>
-- <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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