[gmx-users] Implementation of CHARMM setup in GROMACS

[francesco oteri]

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?

Francesco



2013/2/26 Justin Lemkul <jalemkul at vt.edu>

>
>
> On 2/26/13 11:30 AM, francesco oteri wrote:
>
>> Dear gromacs users,
>> in Bjelkmar et al. (2010) where the implementation of CHARMM in GROMACS is
>> described,
>> the authors say that:
>>
>> "Electrostatics was treated with particle-mesh Ewald (PME), using a
>> short-range cutoff of
>> 1.2 nm, and van der Waals interactions were switched off between 1.0 to
>> 1.2
>> nm."
>>
>> I translated this protocol in the following line in mdp file:
>>
>> ; Neighborsearching
>> rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
>>
>> ; Electrostatics
>> coulombtype     = PME           ; Particle Mesh Ewald for long-range
>> electrostatics
>> rcoulomb           = 1.2           ; short-range electrostatic cutoff (in
>> nm)
>> ;VdW
>> vdwtype            = Switch
>> rvdw                 = 1.2           ; short-range van der Waals cutoff
>> (in
>> nm)
>> rvdw_switch       = 1.0
>>
>> But 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.
>>
>>
>> If I enlarge rlist to 1.3, grompp genrates an error:
>> ERROR 1 [file 02md.mdp]:
>>    With coulombtype = PME, rcoulomb must be equal to rlist
>>    If you want optimal energy conservation or exact integration use
>> PME-Switch
>>
>>
>> So, how can the protocol described in the paper has been implemented?
>>
>>
> Leave rlist at 1.2 and set rlistlong accordingly.  The manual description
> of rlistlong describes this situation.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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-- 
Cordiali saluti, Dr.Oteri Francesco