Hi Justin,<br><br>I used 15 nm cubic box and 6 nm shell.<br>I again tried to insert only 1 histidine molecule in the sphere. I get the same error<br><br>Fatal error:<br>One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.<br>
<br><br><br><div class="gmail_quote">On Sun, May 8, 2011 at 9:53 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
<br>
shivangi nangia wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Justin,<br>
<br>
No.<br>
<br>
I am still preparing the system. I want the protein in the solvent sphere.<br>
<br>
<br>
</blockquote>
<br></div>
I see now. You're setting a 12-nm cubic box, but then using a shell of 6 nm, which causes neighbor searching to occur throughout the entire box. The maximum value of -shell must be less than 1/2 the shortest box vector, so either set up a larger box, or a smaller value of -shell.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
<br>
On Sun, May 8, 2011 at 9:29 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>
shivangi nangia wrote:<br>
<br>
Hello,<br>
<br>
Thanks Justin, I am getting somewhere but still running into<br>
problems.<br>
<br>
Okay, I have a 6 nm sphere (one Li ion surrounded by 1:1<br>
water-methanol mixture) in 12 nm box.<br>
I did the following:<br>
editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro<br>
genbox -cp onlyli.gro -cs mix.gro -shell 6 -o li_sol.gro<br>
<br>
<br>
Then, used genbox -cp protein.gro -cs sphere.gro<br>
with only 1 molecule of histidine I get the same error as with<br>
polyhistidine ( 20 )<br>
<br>
Fatal error:<br>
One of the box vectors has become shorter than twice the cut-off<br>
length or box_yy-|box_zy| or box_zz has become smaller than the<br>
cut-off.<br>
<br>
<br>
I presume this is from mdrun? Your system is collapsing. Without<br>
an .mdp file, it is not possible to diagnose anything.<br>
<br>
-Justin<br>
<br>
How can I resolve this?<br>
<br>
help needed.<br>
<br>
Thanks,<br>
SN<br>
<br>
On Sun, May 8, 2011 at 5:12 PM, Justin A. Lemkul<br>
<<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>><br></div></div><div><div></div><div class="h5">
<mailto:<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>
shivangi nangia wrote:<br>
<br>
Hi Justin and other gmx-users,<br>
<br>
I want to make a sphere around a protein (5nm).with Li<br>
ions and<br>
anions.<br>
<br>
Justin, as you had suggested to use genbox -shell option, I<br>
tried using it but i realized that since my protein is a long<br>
tube like structure, the shell option generated a cyclinder<br>
around the protein.<br>
<br>
The solvent around the protein is 1:1 water-methanol<br>
(pre-prepared mixture n a gro file)<br>
<br>
If I try to start with a ion and solvate it with my<br>
solvent (1:1<br>
water methanol) using -shell option, I do get a sphere<br>
but then<br>
I am unable to insert the protein in the system.<br>
<br>
<br>
And why not?<br>
<br>
genbox -cp protein.gro -cs sphere.gro<br>
<br>
should do exactly what you want, provided the sphere is large<br>
enough<br>
for the protein.<br>
<br>
-Justin<br>
<br>
<br>
Is there another feasible route to get to my desired<br>
configuration of the system ?<br>
<br>
Thanks in advance<br>
<br>
<br>
Best,<br>
SN<br>
<br>
<br>
<br>
<br>
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<br>
Justin A. Lemkul<br>
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ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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Virginia Tech<br>
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ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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