[gmx-users] em.mdp file

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> Lara Bunte wrote:
>> Hello
>>
>> Is this em.mdp file correct for a simple MD simulation?
>>
>> integrator = steep
>>
>> nsteps = 200
>>
>> nstlist = 10
> 
> You should set nstlist=1 for energy minimization (which is not, by 
> definition, MD).
> 

Hit "send" too soon...

You have also specified 200 steps.  This seems arbitrary to me, as there is no 
guarantee that EM will be done at that point.  You also need to specify a value 
for emtol and emstep to be more effective.

There are tutorials linked from the Gromacs webpage.  I'd suggest you work 
through at least one or two of them to understand what the .mdp files are trying 
to achieve and what a proper workflow might be.

-Justin

> 
>> rlist = 1.0
>>
>> coulombtype = pme
>>
>> rcoulomb = 1.0
>>
>> vdw-type = cut-off
>>
>> rvdw = 1.0
>>
>> nstenergy = 10
>>
>>
>> Thanks for help
>> Greetings
>> Lara
>>
> 

-- 
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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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