[gmx-users] tip5p water model:Atomtype LP1 not found

[Justin Lemkul]

On 4/15/13 8:28 AM, Ahmet yıldırım wrote:
> The norm of force is very high. And the system converged in 3 steps
>
> For example, I got the following results for spc water model
> Steepest Descents converged to Fmax < 1000 in 167 steps
> Potential Energy  = -2.1208019e+05
> Maximum force     =  9.8452704e+02 on atom 286
> Norm of force     =  4.9830578e+01
>

Fnorm is not particularly high here or in the previous post.  The fact that it 
converged in 3 steps is also not unexpected.  Minimizing a pure water system 
that is built from pre-equilibrated blocks should be easy.  The potential is 
sensible and the maximum force is below your threshold.  Everything is perfectly 
fine.

-Justin

>
> 2013/4/15 Justin Lemkul <jalemkul at vt.edu>
>
>>
>>
>> On 4/15/13 7:22 AM, Ahmet yıldırım wrote:
>>
>>> I did as you said. I corrected number of water molecules in the topology
>>> by
>>> hand.
>>>
>>> grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o
>>> protein-water.tpr
>>> Steepest Descents converged to Fmax < 1000 in 3 steps
>>> Potential Energy  = -1.5700267e+05
>>> Maximum force     =  7.2195142e+02 on atom 3761
>>> Norm of force     =  1.3341200e+02
>>>
>>> I think these results isnt normal. isnt it?
>>>
>>>
>> What exactly do you think is wrong?
>>
>>
>> -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
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>
>
>

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

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

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