Amit Choubey wrote:
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.
Which version of Gromacs are you using? There was a bug in genbox 4.0.3, but
was fixed prior to 4.0.4.
-Justin
Amit
On Sun, Sep 20, 2009 at 6:38 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Amit Choubey wrote:
Hi everyone,
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?
A segmentation fault with this approach generally indicates that the
requested number of inserted molecules will not fit.
Alternately, you can try -cs spc216.gro -maxsol (your number)
If the second approach also fails, I would think that would be
strong evidence that what you're trying to do won't work.
-Justin
The insert.gro looks like the following
H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=0.31034NM,WFVG,MAR. 1984
3
1SOL OW 1 .130 .128 .113
1SOL HW1 2 .037 .126 .150
1SOL HW2 3 .131 .089 .021
0.31034 0.31034 0.31034
I also tried various other box (larger) sizes for this but it
didnt help.
Thank you in advance.
Amit
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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