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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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