[gmx-users] using 'genbox' for adding solvent
kgp.amit at gmail.com
Mon Sep 21 03:45:08 CEST 2009
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.
On Sun, Sep 20, 2009 at 6:38 PM, Justin A. Lemkul <jalemkul at 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.
> The insert.gro looks like the following
>> H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=0.31034NM,WFVG,MAR. 1984
>> 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.
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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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
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