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

From: Ruth Helena Tichauer <rhtichau.laas.fr>
Date: Mon, 1 Aug 2016 14:38:12 +0200

Thanks a lot for this information, I wouldn’t have thought about!
I’ll do so (and maybe learn about packmol to also give it a try).

Ruth

> On 01 Aug 2016, at 14:11, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> 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
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 01 2016 - 06:00:04 PDT
Custom Search