[gmx-users] Check for bad contacts and/or reduce the timestep

[chris.neale at utoronto.ca]

I believe that Justin was suggesting that you move in the opposite  
direction than to delete some waters.

The number density for water should be about 32.5 waters per cubic  
nanometer, meaning that you should have nearly 1E6 water molecules in  
a cubic box with sides of 31 nm, and 1095 water molecules should have  
a box of 33.7 nm^3 (cubic box with sides of 3.23 nm). I suppose that  
the actual values that you should expect will be slightly lower  
densities because you are not using pbc. And if Justin was right that  
you are reporting angstroms in place of nm, then this makes some sense.

Still, I can't see how genbox could lead to a box with a density that  
is too high -- usually it is somewhat too low. I suggest that you  
diagnose the source of your problem since while simply removing some  
randomly selected waters appears to have worked for you this time,  
that would not be a preferable solution to apply to a system any more  
complex than a single methane in a box of water.

Chris.

-- original message --

Hi,

    You are right, I had to delete some water molecules, it is working  
fine now.

Thanks.

-Nisha P


Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> nishap.patel at utoronto.ca wrote:
>> Hi Justin,
>>
>>  I am trying to plot rdf of one methane molecule in water (spc    
>> water, 1095(water molecule in my file). I did create the file using  
>>   genbox (31.010 31.010 31.010). This is the energy minimization   
>> file  I am using:
>>
>
> Surely a 31-nm cubic box is excessive for a system of 1095 water
> molecules.  You are aware that Gromacs specifies all units in nm, not
> Angstrom, right?
>
> As for the parameters in the .mdp file, I don't see anything that would
> necessarily cause the instability you're seeing.  A better coulombtype
> method (in general) is PME, but this may not have a significant effect
> during the EM procedure.
>
>>
>> title        = Methane in water
>>
>> cpp        = /lib/cpp
>> include        = -I../top
>>
>> 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
>>
>> I tried reducing the steps (to 9 instead of 100) and it works but    
>> it doesn't make sense. I am going to try to build the system again.
>>
>
> Reducing the number of steps will actually make the energy minimization
> worse! If anything, use *more* steps to try to make the structure
> better.
>
> -Justin
>
>> Thanks alot of for help.
>>
>> -Nisha
>>
>>
>> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>>
>>>
>>>
>>> nishap.patel at utoronto.ca wrote:
>>>> Hi, I tried energy minimization and I am getting the error while   
>>>>  I  am running the minimization step. But then I still tried to    
>>>> carry  on with normal md-simulation, and it was fine, but I am    
>>>> sure it  won't give me the result that it should. Is there a    
>>>> reason for  that? I have tried very low energy steps as well, but  
>>>>   I am still  getting the error.
>>>
>>> If minimization still reports the same problems, then what I said
>>> before is still true - you have bad contacts somewhere.  Have you
>>> looked at the trajectory to see where these problematic atoms are and
>>> what might be causing the clashes?
>>>
>>> Sometimes running sufficiently gentle equilibration can relax away some
>>> of these bad contacts, but that is rarely the case and often problems
>>> will manifest later on in the course of MD.  I would seriously consider
>>> re-evaluating however you built your system (which you haven't told us)
>>> and try to get the energy minimization to actually work before just
>>> plowing ahead with fingers crossed.
>>>
>>> -Justin
>>>
>>> -- 
>>> ========================================
>>>
>>> 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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>>
>>
>>
>
> -- 
> ========================================
>
> 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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