[gmx-users] Re: Average box size
Tsjerk Wassenaar
tsjerkw at gmail.com
Tue Jan 4 16:16:10 CET 2011
Navjeet,
The average lengths you already mentioned in your first mail:
>>> Box-X Box-Y Box-Z Volume Density (SI)
>>> 4.44479e+00 4.49781e+00 4.88259e+00 9.76118e+01 1.04364e+03
You also mentioned you used isotropic PC:
>>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
>>> 107.40, 112.20) and Isotropic pressure coupling.
Then the box only gets scaled during the simulation, with no changes
of one vector relative to the other. Then to set the box of your end
structure to match the average volume also means scaling. That means
taking the ratio of the average X-length and the actual X-length, and
feed that as a scaling factor...
Then again, you don't actually need to calculate anything, just think
a little bit harder. You're average box comes with an average density.
editconf has an option to scale the box to get a specific density, so
you can fetch the average density, given above and do:
editconf -f end.gro -o average.gro -density 1.04364e+03
Then go on with your NVT run using average.gro as input (don't forget
the energy minimization!).
Hope it helps,
Tsjerk
On Tue, Jan 4, 2011 at 3:03 PM, Navjeet Ahalawat <navjeet0211 at gmail.com> wrote:
> Hi Tsjerk,
>
> Thanks for your clarifications. I still couldn't follow how I can calculate
> the scaling factor. As I wrote earlier, I ran NPT simulation for equilibration.
>
> Now to start the NVT production run, I need to know the AVERAGE LENGTHS
> (a, b, c) of the triclinic box vectors so that I can generate the
> triclinic box with the
> help of the corresponding angles (88.30, 107.40, 112.20) using the
> command "editconf".
>
> Now I understand that the box-x, box-y, and box-z represents the diagonal
> elements of triangular matrix and the average volume of my triclinic box
> is the product of these diagonal elements. However, as I understand the
> command "editconf" requires the length of the box vectors and the three angles
> to create a triclinic box.
>
> I would greatly appreciate if you could please let me know the command(s) that
> I would require to use to achieve my goal.
>
>
>
>
> Message: 4
> Date: Tue, 4 Jan 2011 12:35:36 +0100
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] Re: Average box size
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTimMYai39NMj6sv008zUuVpT_UHZAvHm=tAH34yK at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Navjeet,
>
> These you had in the log file as you showed in your mail. Note that
> you use isotropic pressure coupling, so you just need to calculate a
> scaling factor, which you can give to editconf to change your system
> to match the average box size.
>
> Cheers,
>
> Tsjerk
>
> On Tue, Jan 4, 2011 at 12:03 PM, Navjeet Ahalawat <navjeet0211 at gmail.com> wrote:
>> Hi Tsjerk,
>>
>> Thanks for reply, Please can you tell me how can I get the average box
>> length (a b c) of my triclinic box for my next step.
>>
>>> Message: 2
>>> Date: Mon, 3 Jan 2011 18:17:15 +0100
>>> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
>>> Subject: Re: [gmx-users] Average box size
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Message-ID:
>>> <AANLkTik2TYHLJVmVFC12260RqkdZnUGe-3kOKigFbM3h at mail.gmail.com>
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>> Hi Navjeet,
>>>
>>> The box is defined as a triangular matrix, so the volume equals the product
>>> of the diagonal elements.
>>>
>>> Hope it helps,
>>>
>>> Tsjerk
>>>
>>> On Jan 3, 2011 5:57 PM, "Navjeet Ahalawat" <navjeet0211 at gmail.com> wrote:
>>>
>>> Hi all
>>>
>>> I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
>>> 107.40, 112.20) and Isotropic pressure coupling. Now i want to use
>>> average box size for production run (NVT). But I am confused because i
>>> am not able to get the meaning of the output values of the log file.
>>>
>>>
>>> Log file output.....
>>>
>>> <====== ############### ==>
>>> <==== A V E R A G E S ====>
>>> <== ############### ======>
>>>
>>> Energies (kJ/mol)
>>> Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
>>> 9.31715e+02 2.35558e+03 1.63083e+02 5.15266e+03 1.79003e+03
>>> Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
>>> 1.63211e+04 2.86765e+04 -1.72320e+05 -4.98704e+04 -1.66800e+05
>>> Kinetic En. Total Energy Temperature Pressure (bar) Cons. rmsd ()
>>> 1.27874e+04 -1.54012e+05 1.49958e+02 1.07033e+00 0.00000e+00
>>>
>>> Box-X Box-Y Box-Z Volume Density (SI)
>>> 4.44479e+00 4.49781e+00 4.88259e+00 9.76118e+01 1.04364e+03
>>>
>>> If Box-X Box-Y Box-Z represent average value of a b c then volume
>>> does not correspond to my triclinic box because its just
>>> multiplication of Box-X Box-Y Box-Z. So Please can anybody help me
>>> which volume should I consider for next NVT production run.
>>>
>>> Any help in this regard would be highly appreciated.
>>>
>>>
>>> Thanks & Regards,
>>> Navjeet Ahalawat
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
>
> ------------------------------
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
More information about the gromacs.org_gmx-users
mailing list