[gmx-users] Re: Average box size

Navjeet Ahalawat navjeet0211 at gmail.com
Tue Jan 4 15:03:26 CET 2011

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>
       <AANLkTimMYai39NMj6sv008zUuVpT_UHZAvHm=tAH34yK at mail.gmail.com>
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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.



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
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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


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