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

[Amit Choubey]

yes you are right its a bug, everything works well on the most recent
version.
Thank you

On Sun, Sep 20, 2009 at 6:55 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 <jalemkul at vt.edu<mailto:
>> 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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>>
>>    --    ========================================
>>
>>    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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