Dear Bill,
Thank you for your reply!
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,
>>
>> Thank you for your answer!
>>
>> 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
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>>>>
>>>
>>>
>>> --
>>> *Bilal Nizami*
>>> School of Health Sciences
>>> University of KwaZulu-Natal
>>> Durban
>>> 4000
>>> South Africa
>>>
>>> Linkedin: za.linkedin.com/pub/bilal-nizami/49/673/790/
>>> Email: 214573074.stu.ukzn.ac.za
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>>>
>>
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Received on Mon Aug 01 2016 - 05:00:04 PDT
