[gmx-users] Fwd: Questions for the forum

[Justin Lemkul]

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

==================================================