[gmx-users] Implementation of CHARMM setup in GROMACS

[francesco oteri]

I downloaded and installed gromacs-4.6
but I get the warning

WARNING 1 [file NVE.mdp]:
  The sum of the two largest charge group radii (0.067845) is larger than
  rlist (1.200000) - rvdw (1.200000)

I attacch the files you may need to solve the problem
 NVE.mdp <https://docs.google.com/file/d/0B1ktZ-u2OHFAdUl6UkFJajNGcGs/edit>

 processed.top<https://docs.google.com/file/d/0B1ktZ-u2OHFAcG82WnltVmdFN1U/edit>

 01em.gro <https://docs.google.com/file/d/0B1ktZ-u2OHFAZ0d3WGs3U1dBaU0/edit>

 index.ndx<https://docs.google.com/file/d/0B1ktZ-u2OHFAemxNc0c5YlRlNlE/edit>



2013/2/26 francesco oteri <francesco.oteri at gmail.com>

> Thank you so much for the help!
>
>
> 2013/2/26 Justin Lemkul <jalemkul at vt.edu>
>
>>
>>
>> On 2/26/13 12:01 PM, francesco oteri wrote:
>>
>>> I am using 4.5.5...Is it OK?
>>>
>>>
>> If it's giving a note about that, then clearly not.  Try 4.6.  But as I
>> said, there's nothing actually wrong.
>>
>> -Justin
>>
>>
>>> 2013/2/26 Justin Lemkul <jalemkul at vt.edu>
>>>
>>>
>>>>
>>>> On 2/26/13 11:47 AM, francesco oteri wrote:
>>>>
>>>>  Thank you Justin,
>>>>> I added
>>>>> rlistlong       = 1.4
>>>>>
>>>>> but still grompp complains:
>>>>> NOTE 1 [file 02md.mdp]:
>>>>>     For energy conservation with switch/shift potentials, rlist should
>>>>> be
>>>>> 0.1
>>>>>     to 0.3 nm larger than rvdw.
>>>>>
>>>>> Why doesn't grompp looks for rlistlong value?
>>>>>
>>>>>
>>>>>  There was a problem with an older version of Gromacs (I can't remember
>>>> which) where grompp ignored rlistlong.  It has no implication for mdrun
>>>> and
>>>> is solved by using the newest version.
>>>>
>>>>
>>>> -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://vt.edu/Pages/Personal/justin>
>>>> <h**ttp://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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>



-- 
Cordiali saluti, Dr.Oteri Francesco