[gmx-users] Cannot minimiza - vdwradii.dat ???

[Justin Lemkul]

On 11/15/12 9:03 AM, Steven Neumann wrote:
> On Thu, Nov 15, 2012 at 1:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 11/15/12 8:41 AM, Steven Neumann wrote:
>>>
>>> Dear Gmx Users,
>>>
>>> I am trying to run simulations of protein and FE(2+) atoms. I placed
>>> them randomly around the protein, solvated the system and tried to
>>> minimize. After grompp, I tried mdrun:
>>>
>>> Stepsize too small, or no change in energy.
>>> Converged to machine precision,
>>> but not to the requested precision Fmax < 1000
>>>
>>> Double precision normally gives you higher accuracy.
>>> You might need to increase your constraint accuracy, or turn
>>> off constraints alltogether (set constraints = none in mdp file)
>>>
>>> Steepest Descents converged to machine precision in 62 steps,
>>> but did not reach the requested Fmax < 1000.
>>> Potential Energy  = -7.2573600e+05
>>> Maximum force     =  5.7863950e+05 on atom 756
>>> Norm of force     =  3.5862925e+03
>>>
>>> I tried different stepsizes, constarint = none etc but never converged
>>> to requested Fmax < 1000
>>>
>>> When I try NVT:
>>>
>>> Fatal error:
>>> 2 particles communicated to PME node 0 are more than 2/3 times the
>>> cut-off out of the domain decomposition cell of their charge group in
>>> dimension x.
>>> This usually means that your system is not well equilibrated.
>>>
>>>
>>> So the problem is with minimization.
>>>
>>> My question: Can it be the problem of not specified vdwradius of my
>>> FE(2+) in vdwradii.dat ? I mean, can ater molecules overlap with
>>> Ferrous and thus minimization does not converge?
>>>
>>
>> The problem is unrelated to vdwradii.dat, which is only used for neighbor
>> searching with genbox.  mdrun tells you there is a problem with atom 756.
>> What is it?  What is it interacting with?  That's how you trace the problem.
>>
>> -Justin
>>
>
> This is Fe(2+) - from trjactory it can be observed that it collides
> with negatively charged oxygen from my other small molecule. Are you
> sure that vdwradii.dat wont solve it while placing molecules using
> genbox and then solvating. The vdw radius of Fe(2+) is 2 A. Would you
> suggest something?
>

Try it and see.  If genbox doesn't find a radius, it uses a default value, which 
is specified with -vdwd on the command line, so modifications to vdwradii.dat 
are not strictly necessary, but a more explicit command might be.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================