[gmx-users] Reducing density using -vdwd option for a new solvent in the system

[shivangi nangia]

Thanks Justin, vdwradii.dat suggestion worked :)



On Mon, Jun 13, 2011 at 11:05 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> shivangi nangia wrote:
>
>> Hello dear gmx-users,
>>
>> I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as
>> the solvent ( with a positively charged protein and few DHB anions) in a
>> box.
>>
>> I have created the .itp and .gro file of DHB using PRODRG.
>>
>>
> Unrelated advice - the topology is probably useless unless you've corrected
> the charges.  See the paper linked from:
>
> http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
>
>
>  I am able to create the system, but when I try to energy minimize the
>> system I get the message:
>>
>> Steepest Descents:
>>   Tolerance (Fmax)   =  1.00000e+01
>>   Number of steps    =        50000
>> Step=   14, Dmax= 1.2e-06 nm, Epot=  9.04353e+19 Fmax=         inf, atom=
>> 2781
>> Stepsize too small, or no change in energy.
>> Converged to machine precision,
>> but not to the requested precision Fmax < 10
>>
>> Double precision normally gives you higher accuracy.
>>
>> writing lowest energy coordinates.
>>
>> Back Off! I just backed up em.gro to ./#em.gro.1#
>>
>> Steepest Descents converged to machine precision in 15 steps,
>> but did not reach the requested Fmax < 10.
>> Potential Energy  =  9.0435262e+19
>> Maximum force     =            inf on atom 2781
>> Norm of force     =            inf
>>
>>
>> The reason behind this was that DHB molecules were on top of each other,
>> highly dense system ( viewed in VMD)
>> So, to reduce the density of DHB molecules, I tried using-vdwd option of
>> genbox (changed from default value of 0.105 to 0.5)
>> But, I got almost same number of DHB molecules using genbox.
>>
>>
> The -vdwd option has no effect unless you're using atom names that are not
> found in vdwradii.dat (see the genbox help description).  Your DHB molecule
> should be unaffected by the use of -vdwd.
>
>
>
>> What is the best solution to this problem as I understand, reducing the
>> density of DHB molecules around the protein as a solvent or there is some
>> other problem?
>>
>>
> You need to generate a configuration in which molecules aren't overlapping.
> There are several ways to accomplish this.  You can manually place molecules
> within a box at a desired location with editconf -center, otherwise genbox
> -ci -nmol.  If the locations of the molecules are not what you desire with
> genbox, change the value of -seed and try again.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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