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

Tue Jan 5 20:53:22 CET 2016

On 1/5/16 2:51 PM, Chang Woon Jang wrote:
> Dear Justin,
>
>   Please take a look at the file. I modified mdp file provided from VOTCA
> tutorial. I think that mdp file is ok.
>

The mailing list does not accept attachments.  Copy and paste the .mdp contents.

-Justin

> 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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>>>>>>>> posting!
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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
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
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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
>>>
>>> * Please search the archive at
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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

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