[gmx-users] charmm in gromacs cut-offs

[Justin Lemkul]

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
>    interactions!
>
> 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
>
> http://redmine.gromacs.org/issues/1164
>
> 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 
problems.

-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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