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

[Justin A. Lemkul]

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

-- 
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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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