[gmx-users] charmm in gromacs cut-offs
jalemkul at vt.edu
Sat May 18 20:46:38 CEST 2013
On 5/18/13 7:58 AM, tarak karmakar wrote:
> Dear All,
> It seems the problem in the cut-off schemes while using charmm force
> field in gromacs persists even in the latest gromacs-4.6.1 version.
> Recently I have posted regarding this problem came in gromacs-4.5.5
> version. If anybody has already tested this issue in the latest version,
> please leave a comment in the mailing list.
> The cut-off parameters I have used are as follows
> rlist = 1.2
> rlistlong = 1.4
> ; 7.3.10 Electrostatics
> coulombtype = PME
> rcoulomb = 1.2
> ; 7.3.11 VdW
> vdwtype = switch
> rvdw = 1.2
> rvdw-switch = 1.0
> NOTE 3 [file md_sim_ann.mdp]:
> The switch/shift interaction settings are just for compatibility; you
> will get better performance from applying potential modifiers to your
> NOTE 4 [file md_sim_ann.mdp]:
> For energy conservation with switch/shift potentials, rlist should be 0.1
> to 0.3 nm larger than rvdw.
> NOTE 5 [file md_sim_ann.mdp]:
> The sum of the two largest charge group radii (0.079732) is larger than
> rlist (1.200000) - rvdw (1.200000)
> This part is reported as bug in gromacs -4.5.5 and required to be verified
> by users through their feedback
> In this link it is showing affected version grom-4.6.1 !!
There are a lot of conditionals that are evaluated and probably (as Mark has
indicated) some of them are conflicting. What you have posted above seems
correct from my interpretation of everything I have read about using CHARMM.
Since all you are getting are notes (rather than errors), you shouldn't have any
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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