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

[Chang Woon Jang]

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.

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,
>>>> --
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>>>
>>>
>>> --
>>> || radhe radhe ||
>>>
>>> abhishek
>>> --
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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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