[gmx-users] Fwd: Questions for the forum

Thu Oct 13 15:49:51 CEST 2016

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 <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
>>>>
>>>> jalemkul at 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
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
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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

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