On 10/13/16 9:45 AM, Matilde Viegas wrote:
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.


You need to provide your exact commands, copied and pasted from the terminal. You can't just say you did my tutorial, because there's a lot of differences in what you actually did and what's in that example.

One thing that is unclear is if you're trying to import an already-solvated system from AMBER into GROMACS. If you are, then you shouldn't be re-sizing the box or adding any more water. But again, only your exact commands and descriptions of file contents will tell us anything productive.

-Justin

2016-10-13 14:40 GMT+01:00 Justin Lemkul <jalem...@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 <jalem...@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 <ddhe...@gmail.com>:


You can reduce your box size to get a smaller system.


On 13 October 2016 at 17:41, Matilde Viegas <matildefrvie...@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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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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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http://mackerell.umaryland.edu/~jalemkul

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