[gmx-users] Implementation of CHARMM setup in GROMACS

[francesco oteri]

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
>>>
>>> --
>>> ==============================****==========
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>>>
>>> Justin A. Lemkul, Ph.D.
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>>> Virginia Tech
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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