[gmx-users] Avoiding parameterization step
ggroenh at gwdg.de
Tue Mar 11 12:11:37 CET 2008
> Thank you very much for your response. I am at the moment interested in doing conformational search.
Using freeze groups in combination with conformational search does not
> Is there any good paper that explain nicely about doing the charge distribution calculation?
You need to do an ab initio calculation on the system you want to
parametrize. This will give you the true charge distribution to which
you can fit a set of partial charges located on the nuclei. There are
several possibilities to do the fitting, check what the QM programs you
can use support. But in the end the charges are not too strongly
dependent on the fitting/level of QM. In addition you can sample several
configurations and use some sort of averaging to get the partial charge
> With regards,
>> Date: Tue, 11 Mar 2008 10:16:51 +0100
>> From: ggroenh at gwdg.de
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Avoiding parameterization step
>>> Hi All User,
>>> I have been wondering whether it is advisable to avoid parametrization step by freezing the atoms in MD
>> Depends on what you want to do.
>> You most likely would still need the charge distribution, which is the
>> most difficult part of the parametrization part usually.
>> Bonded interactions can often be guessed by comparing to known residues.
>>> With regards,
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