[gmx-users] g_dipoles

rams rams rams.crux at gmail.com
Tue Mar 17 15:44:47 CET 2009

```Dear David,

The peptide is having a -ve charge of 3. Though the components might
dependent upon the orientation but the average might be the same
irrespective of the orientation I suppose.

Ram.

On Tue, Mar 17, 2009 at 3:54 AM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> rams rams wrote:
>
>> Dear Users,
>>
>> I am trying to obtain the dipole moment of a 40 amino acid residue peptide
>> using g_dipoles. I am getting a huge number (about 700 Debye). I expect it
>> to be around 150 Debye (based on other studies). To make sure it I extracted
>> a shapshot of the structure and obtained the dipolemoment using the
>> following command:
>>
>> g_dipoles -f ab42_1.0_30ns.pdb -s MD_ab42.tpr -o Mtot.xvg  -n prot_dip.ndx
>>
>> I am giving the last few lines of the output below:
>>
>> Dipole moment (Debye)
>> ---------------------
>> Average  = 516.7213  Std. Dev. =   0.0000  Error =   0.0000
>>
>> The following averages for the complete trajectory have been calculated:
>>
>>  Total < M_x > = -54.3459 Debye
>>  Total < M_y > = 12.8373 Debye
>>  Total < M_z > = 513.695 Debye
>>
>>  Total < M_x^2 > = 2953.47 Debye^2
>>  Total < M_y^2 > = 164.796 Debye^2
>>  Total < M_z^2 > = 263883 Debye^2
>>
>>  Total < |M|^2 > = 267001 Debye^2
>>  Total < |M| >^2 = 267001 Debye^2
>>
>>  < |M|^2 > - < |M| >^2 = 0 Debye^2
>>
>> Finite system Kirkwood g factor G_k = 0
>> Infinite system Kirkwood g factor g_k = 0
>>
>> Epsilon = 1
>>
>> The same structure (i.e., what i have used in the above command) if I open
>> and check for the dipole moment using YASARA suite of program it is showing
>> as 173 Debye. Which is reasonable. Am I making any mistake while obtaining
>> the dipole moment using g_dipoles or I am looking at the wrong file ??
>>
>
> Is the peptide neutral? Otherwise the result might be orientation
> dependent.
>
>
>
>> Thanks.
>>
>> Ram.
>>
>>
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>>
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>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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