[gmx-users] Implementation of CHARMM setup in GROMACS

[Justin Lemkul]

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

-- 
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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

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