[gmx-users] Fwd: Questions for the forum

[Matilde Viegas]

Of course, sorry!
I followed your lyzosyme tutorial, the exact same commands, only addapting
it to my system (force field, tip3p water, just like I did on AMBER), box
was dodechaedron, 1.2nm. I didn't alter anything beside that... My enzyme
is around 72 thousand atoms, after adding the solvation box, it goes up to
2.5 million atoms.

2016-10-13 14:40 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 10/13/16 9:38 AM, Matilde Viegas wrote:
>
>> Yes, I noticed that! I said 10, referring to angstrom, in the input I had
>> 1.0nm.
>>
>> So you probably think it is only some error in the input, not really
>> something I can tackle, right? I really can't figure it out...
>>
>>
> Without seeing your exact sequence of commands, there's nothing we can do
> to help.  The only thing consistent with having an unexpected million-atom
> system is that you set up the box incorrectly with editconf.  But you
> haven't told us exactly what you've done...
>
> -Justin
>
>
> Thank you for your time, Justin
>>
>> 2016-10-13 13:04 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>>>
>>> On 10/13/16 7:34 AM, Matilde Viegas wrote:
>>>
>>> I tried to downzise to 10 and yet the reduction was very little. I was
>>>> just
>>>> trying t understand how can the difference between the same systems,
>>>> using
>>>> either AMBER or GROMACS, can be of 1 million atoms...
>>>>
>>>>
>>>> GROMACS uses SI units, so distances/box vectors are specified in nm, not
>>> Angstrom.  See Chapter 2 of the manual for unit conventions.
>>>
>>> -Justin
>>>
>>>
>>> 2016-10-13 12:27 GMT+01:00 Dd H <ddhecnu at gmail.com>:
>>>
>>>>
>>>> You can reduce your box size to get a smaller system.
>>>>
>>>>>
>>>>> On 13 October 2016 at 17:41, Matilde Viegas <matildefrviegas at gmail.com
>>>>> >
>>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>>>
>>>>>> my name is Matilde. This is my first time using GROMACS. I'm switching
>>>>>>
>>>>>> from
>>>>>
>>>>> AMBER to GROMACS however I'm having some trouble reproducing my system:
>>>>>>
>>>>>> In AMBER, I'm working with a 5000 residues protein, a water box (TIP3)
>>>>>> of
>>>>>> 12A, roughly 1.5 million atoms total. I tried building the same system
>>>>>> in
>>>>>> GROMACS, cubic box, 12A, same protein, however I obtain a 2.5 million
>>>>>>
>>>>>> atoms
>>>>>
>>>>> system. Is there a way I can reduce the number of atoms?
>>>>>>
>>>>>> Thank you in advance,
>>>>>> Matilde
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
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>>>>>>
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>>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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