[gmx-users] Fwd: Questions for the forum

[Matilde Viegas]

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...

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
>>>> --
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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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