[gmx-users] Implementation of CHARMM setup in GROMACS

[Justin Lemkul]

On 2/26/13 2:06 PM, francesco oteri wrote:
> 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>
>

Perhaps the previously fixed issue isn't perfect, but again this is the same 
symptom where apparently rlistlong is not being fully interpreted.  There should 
be nothing wrong if you have an adequate setting for rlistlong.

-Justin

>
>
> 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
>>
>
>
>

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

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

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