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

[nishap.patel at utoronto.ca]

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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