[gmx-users] Which coulmbtype?
feenstra at chem.vu.nl
Wed Jan 7 08:36:01 CET 2004
David van der Spoel wrote:
> On Mon, 5 Jan 2004, Raj Badhan wrote:
>>Thank you for your response.
>>I have had a look at the g_mindist, and have found out that the
>>minimum distance is aprox 4.7nm.
>>When I come to paramatise this in the mdp file, should I use values
>>around this (i.e. 5 ) for rcoulomb/rvdw/rlist?
> No, I think this means that you want the box to be 5 nm, and cut-offs can
> be simply in the normal range (1.4,1.4,0.9)
No, if Raj did g_mindist -pi, it means he has at least 4.7 nm of water
inbetween periodic images of the ATP. That is, however, extremely
large. Are you sure you didn't mean 4.7 Angstrom (i.e., 0.47 nm, which
would be too small)?
But, in any case, this value has no other relation to the cut-offs (rcoul,
rvwd & rlist) than that you need it to be larger than the cut-offs. Whether
it is a few tenths of nm larger, or three times larger doesn't matter.
> Is this the ATP/protein complex? Or pure ATP in water?
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