[gmx-users] Fwd: Questions for the forum

Justin Lemkul jalemkul at vt.edu
Thu Oct 13 15:40:27 CEST 2016



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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>> --
>> ==================================================
>>
>> 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

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


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