# Re: [AMBER] Sander bomb: how to create a larger box

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Mon, 1 Aug 2016 05:11:10 -0700

You will probably want to avoid having the box scale (constant pressure)
when you are equilibrating the extra waters, since that could lead to a
discontinuity when you splice with the original system and likely atom
overlap and blowup. This makes it impossible to get the density right by
the usual method, adding to the burden equilibration must carry when you
start it all moving together. That's assuming you use leap to add the
waters. I would look at packmol (haven't tried it myself) to see if it
will pack waters better to your desired box.

Bill

On 8/1/16 4:42 AM, Ruth Helena Tichauer wrote:
> Dear Bill,
>
>
> It would save me two months' work so I guess I’ll try this out and I hope it will work without a huge bias of the results..
>
> Best regards,
>
> Ruth
>
>
>> On 01 Aug 2016, at 13:32, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>
>> An AI prof once told our class that many people had competed long and
>> hard to come up with the best algorithm for restacking a pile of blocks
>> in a specified order. In the end it was decided that it was generally
>> sufficient to knock them all down and stack them from there. The
>> principle may apply here, but one thing you could do is generate a pdb
>> of your restrt, load it in leap, solvate it hoping it keeps its
>> orientation so you get a uniform layer of fresh water, run dynamics with
>> the original system held fixed with belly to get semi-valid velocities,
>> then cut out the new crds and velocities (e.g. with awk or perl) and
>> patch them into the respective sections of a copy of the original
>> restrt. Then you would have to equilibrate the new system and wonder if
>> all that biased your results. I might consider it if it would save a
>> week's work or more.
>>
>> Bill
>>
>>
>> On 8/1/16 3:53 AM, Ruth Helena Tichauer wrote:
>>> Dear Bilal,
>>>
>>>
>>> Indeed, that’s what I had first thought.. but I was hoping for a solution anyway, and I figured out a scheme such that:
>>>
>>> As the numbering of the water molecules assigned by tleap would be the same, I would replace the new coordinates of the water molecules by the ones on the restart file and, as there would be more water molecules than previously, I would keep the coordinates assigned by tleap for these extra water molecules (and hopefully there would be a way to also get velocities for these extra water molecules).
>>>
>>> I thought that such a procedure would be achievable with parmed and so I was hoping some guiding to do so.. Does anyone know if this would be possible?
>>>
>>> Thanks in advance for any suggestion,
>>>
>>> Ruth
>>>
>>>
>>>> On 30 Jul 2016, at 22:58, Bilal Nizami <nizamibilal1064.gmail.com> wrote:
>>>>
>>>> Dear Ruth,
>>>>
>>>> According to my understand, this is not possible. If you remove the water
>>>> molecule from your trajectory and introduce new ones, new water molecules
>>>> would have different coordinates than those in your restart file. I guess,
>>>> program won't be able to resolve this.
>>>>
>>>> Regards,
>>>>
>>>> 2016-07-28 16:48 GMT+02:00 Ruth Helena Tichauer <rhtichau.laas.fr>:
>>>>
>>>>> Dear amber users,
>>>>>
>>>>> I am running a QM/MM molecular dynamics simulation and I get the following
>>>>> error message:
>>>>>
>>>>> SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>
>>>>> QM region + cutoff larger than box
>>>>> cannot continue, need larger box.
>>>>>
>>>>> I understand why this is happening and to solve this behaviour I wish to
>>>>> create a larger water box around my protein rather than decrease the value
>>>>> of the cutoff.
>>>>>
>>>>> I was thinking to strip all the water molecules and then create a new box
>>>>> and new parameters with tleap but then, if I understand correct, I would
>>>>> have to start all over (starting from 0 ps). So, is there any way such
>>>>> that, I would be able to have a bigger water box and use the restart file
>>>>> from the previous run in order to continue my simulation from where it has
>>>>> been stopped?
>>>>>
>>>>> Thank you for any help,
>>>>>
>>>>> Ruth
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>> --
>>>> *Bilal Nizami*
>>>> School of Health Sciences
>>>> University of KwaZulu-Natal
>>>> Durban
>>>> 4000
>>>> South Africa
>>>>
>>>> Email: 214573074.stu.ukzn.ac.za
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Received on Mon Aug 01 2016 - 05:30:03 PDT
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