[gmx-users] Error during minimization

[Mark Abraham]

nishap.patel at utoronto.ca wrote:
> I have a question regarding the simulations that I am running. I tried 
> creating a pdb file with one methane and water molecules, but the system 
> keeps showing 'bad contact' error when I run the minimization step and I 
> don't understand what I am doing wrong.
> 
>  This is my methane file :
> 
> TITLE     methane  in water
> CRYST1   33.010   33.010   33.010  90.00  90.00  90.00 P 1           1
> MODEL        1
> ATOM      1  CH4 CH4     1      19.520  25.090  16.410  1.00  0.00
> 
> So I use this file and run editconf -f methane1.pdb -o box.pdb -bt 
> cubic. This creates a
> box with volume of around 35 nm^3
> 
> Then I add water molecules using :
> 
> genbox -cp box.pdb -cs spc216 -o methwa.pdb -p topol.top
> 
> This adds around 1191 water molecules to the existing methane file. So 
> my box is now
> (33.010 33.010 33.010 with total 1192 molecules). 

Please read genbox -h about the mechanism it uses to avoid 
intermolecular clashes, and how that might not be working for your 
united-atom case.

Mark

> Then I run 
> minimization on this system
> using minim.mdp as follows:
> 
> integrator        = steep
> emtol                = 1.0
> nsteps                = 100
> nstenergy        = 10
> nstxtcout        = 10
> xtc_grps        = CH4 SOL
> energygrps        = CH4 SOL
> nstlist                = 5
> ns_type                = simple
> rlist                = 1.0
> coulombtype        = cut-off
> rcoulomb        = 1.0
> rvdw                = 1.0
> constraints        = none
> pbc                = no
> 
> grompp -f minim.mdp -c methwa.pdb -p topol.top -v
>  mdrun -v
> 
> And it runs minimization with bad contact errors and this is the result 
> I get:
> Steepest Descents converged to machine precision in 32 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  = -4.9481789e+04
> Maximum force     =  3.2827865e+06 on atom 500
> Norm of force     =  6.9951227e+04
> 
> 
> Any suggestions?
> 
> Nisha.P
>