[gmx-users] using 'genbox' for adding solvent

[Amit Choubey]

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.
Amit

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.
>
> -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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>>
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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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