[gmx-users] Implementation of CHARMM setup in GROMACS

Tue Feb 26 21:40:25 CET 2013

That looks like (at least) a grompp bug leading to the error. Can you
attach a .tpr file to http://redmine.gromacs.org/issues/1164 please
Francesco?

Mark

On Tue, Feb 26, 2013 at 8:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<https://docs.google.com/file/d/0B1ktZ-u2OHFAdUl6UkFJajNGcGs/edit>
>> >
>>
>>   processed.top<https://docs.**google.com/file/d/0B1ktZ-**
>> u2OHFAcG82WnltVmdFN1U/edit<https://docs.google.com/file/d/0B1ktZ-u2OHFAcG82WnltVmdFN1U/edit>
>> >
>>
>>   01em.gro <https://docs.google.com/file/**d/0B1ktZ-**
>> u2OHFAZ0d3WGs3U1dBaU0/edit<https://docs.google.com/file/d/0B1ktZ-u2OHFAZ0d3WGs3U1dBaU0/edit>
>> >
>>
>>   index.ndx<https://docs.google.**com/file/d/0B1ktZ-**
>> u2OHFAemxNc0c5YlRlNlE/edit<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<http://vt.edu/Pages/Personal/justin>
>>>>>> >
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>>>>>> http://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://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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>>>>
>>>
>>>
>>> --
>>> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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