[gmx-users] How to adjust the box size to correct density?

Chang Woon Jang changwoonjang at gmail.com
Tue Jan 5 20:51:46 CET 2016


Dear Justin,

 Please take a look at the file. I modified mdp file provided from VOTCA
tutorial. I think that mdp file is ok.

Thank you very much.

Best regards,
Changwoon Jang

On Tue, Jan 5, 2016 at 2:45 PM, Chang Woon Jang <changwoonjang at gmail.com>
wrote:

> Dear Justin,
>
>  Please take a look at the files. I modified mdp file provided from VOTCA
> tutorial. I think that mdp file is ok.
>
> I also attached full topology files as well.
>
> Thank you very much.
>
> Best regards,
> Changwoon Jang
>
>
> On Tue, Jan 5, 2016 at 2:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/5/16 2:25 PM, Chang Woon Jang wrote:
>>
>>> Dear Justin,
>>>
>>>     I am curious about resizing the box. My system contains 15000 atoms
>>> representing liquid polymer with very low density (maybe gas phase due to
>>> very low density). Does this very low density affect the simulation not
>>> to
>>> converge the box? Or, do the initial conditions (Pcoupl=berendsen,
>>> Pcoupltype=isotropic, tau_p=5.0, compressibility=4.5e-5, ref_p=1.0) in
>>> gromapp.mdp affect? Do I need to test these conditions? I am just
>>> starting
>>> to use GROMACS for obtaining atomistic trajectory compatible with VOTCA
>>> coarse-graining package.
>>>
>>>
>> Those settings should be fine.  Extract the box vectors from the .edr
>> file and see how much they fluctuate; the final snapshot is not necessarily
>> representative.  But the fact that the box size is exactly the same from
>> start to finish suggests there is something incorrect (or at least, really
>> weird) going on.  Provide the full text of your .mdp please, not just the
>> section you think is relevant.
>>
>> -Justin
>>
>>
>> The same configuration in LAMMPS works fine.
>>>
>>> Thank you.
>>>
>>> Best regards,
>>> Changwoon Jang
>>>
>>> On Tue, Jan 5, 2016 at 1:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 1/5/16 1:42 PM, Chang Woon Jang wrote:
>>>>
>>>> Dear Abhishek Khetan,
>>>>>
>>>>>     Thank you for your answer. It means that Gromacs does not
>>>>> automatically
>>>>> adjust the box size even though NPT ensemble is employed. Am I right?
>>>>>
>>>>>
>>>>> This is incorrect.  The box size will change under the influence of
>>>> pressure. Its shape should be conserved.  But if you're seeing the exact
>>>> same box vectors before and after the simulation, something went wrong
>>>> with
>>>> your input.
>>>>
>>>> Different from Gromacs, Lammps automatically adjust box size when NPT
>>>>
>>>>> ensemble is applied during the simulation. Therefore, the density is
>>>>> able
>>>>> to be fitted with initial conditions (pressure, temperature, simulation
>>>>> time).
>>>>>
>>>>>
>>>>> GROMACS does this, too.
>>>>
>>>> When I used the "gmx editconf" to resize the box to correct a density,
>>>> vmd
>>>>
>>>>> shows a very ugly configurations. I think that topology file will check
>>>>> the
>>>>> bond informations no matter how the gro file, containing only atom
>>>>> coordinates and box size, looks like.
>>>>>
>>>>>
>>>>> Indeed, editconf is not useful here.  It scales coordinate positions to
>>>> achieve the desired density.  This is not what you want.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> If I am wrong, please correct me.
>>>>
>>>>>
>>>>> Thank you.
>>>>>
>>>>> Best regards,
>>>>> Changwoon Jang
>>>>>
>>>>> On Tue, Jan 5, 2016 at 1:16 PM, abhishek khetan <askhetan at gmail.com>
>>>>> wrote:
>>>>>
>>>>> To rescale the box.gro to a desired size using the actual density
>>>>> 543.21
>>>>>
>>>>>> kg/l of the solvent and get a new scaled.gro file, I use this command:
>>>>>>
>>>>>> $ gmx editconf -f box.gro -density 543.21 -o scaled.gro > logfile
>>>>>>
>>>>>>
>>>>>> On Tue, Jan 5, 2016 at 7:05 PM, Chang Woon Jang <
>>>>>> changwoonjang at gmail.com
>>>>>>
>>>>>>>
>>>>>>> wrote:
>>>>>>
>>>>>> Dear Gromacs Users,
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I have a low density polymer system initially. I would like to fit
>>>>>>> the
>>>>>>> correct liquid density using NPT simulation.
>>>>>>>
>>>>>>> I used Pcoupl=berendsen for 22 ns but the box size in confout.gro is
>>>>>>>
>>>>>>> still
>>>>>>
>>>>>> the same as the input size of conf.gro.
>>>>>>>
>>>>>>> Initial in conf.gro (10.0 10.0 9.8)
>>>>>>> output in confout.gro (10.0 10.0 9.8)
>>>>>>>
>>>>>>> My initial conditions are
>>>>>>>
>>>>>>> tau_p=5.0
>>>>>>> compressibility=4.5e-5
>>>>>>> ref_p=1.0
>>>>>>>
>>>>>>> Do I need to increase compressibility?
>>>>>>>
>>>>>>> Thank you.
>>>>>>>
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Changwoon Jang,
>>>>>>> --
>>>>>>> Gromacs Users mailing list
>>>>>>>
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>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> || radhe radhe ||
>>>>>>
>>>>>> abhishek
>>>>>> --
>>>>>> 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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>>>> 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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>> Gromacs Users mailing list
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>


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