[gmx-users] Implementation of CHARMM setup in GROMACS
francesco.oteri at gmail.com
Tue Feb 26 17:47:03 CET 2013
Thank you Justin,
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?
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
>> 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
>> 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
>> rcoulomb = 1.2 ; short-range electrostatic cutoff (in
>> vdwtype = Switch
>> rvdw = 1.2 ; short-range van der Waals cutoff
>> rvdw_switch = 1.0
>> But grompp complains:
>> NOTE 1 [file 02md.mdp]:
>> For energy conservation with switch/shift potentials, rlist should be
>> 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
>> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
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Cordiali saluti, Dr.Oteri Francesco
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