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

[shivangi nangia]

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.

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.


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?

Thanks in advance,
SN
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