VMD-L Mailing List

From: Wenhao Liu (mdsimulate_at_gmail.com)
Date: Wed Apr 17 2013 - 13:17:42 CDT

Thank you so much for your patient helping!

Best
Wenhao

On Wed, Apr 17, 2013 at 2:14 PM, Mayne, Christopher G
<cmayne2_at_illinois.edu>wrote:

> Water molecules that appear to fly off into space are simply not finding
> an energy minimum and should be ignored during the optimization
>
>
> On Apr 17, 2013, at 1:11 PM, Wenhao Liu wrote:
>
> Chris,
> Thanks so much for making this clear. Last quick question, when I finished
> water-complexe gaussian calculation and load them into vmd, if in one
> trajectory water away from the complex farther and farther and seems never
> reach equilibrium. Is this mean this donor(or acceptor) bonding should not
> be included in charge optimization, then I just abandon it in charge
> optimization?
>
> On Wed, Apr 17, 2013 at 1:51 PM, Mayne, Christopher G <
> cmayne2_at_illinois.edu> wrote:
>
>> The MM values will never match the QM values. The idea is to
>> compromise so that the charges are not too far from QM while performing as
>> well as possible in an MM simulation. It is not always necessary to use
>> all three files, based on the 3D topology of your molecule and other
>> symmetry arguments. You should try to use the target data from at least
>> one of the 120 positions, in addition to the 180 position.
>>
>> Christopher Mayne
>>
>>
>> On Apr 17, 2013, at 12:46 PM, Wenhao Liu wrote:
>>
>> Chris,
>> I read the CGenFF paper and I think it didn't discuss much about carbonyl
>> group. So you mean the reason why ffTK generate three water-molecule
>> complexes for oxygen in carbonyl group is to let MM values approach QM
>> values, right? So when I optimize the charges in ffTK for the moelcule
>> contain carbonyl group, I should use all these three(120a, 120b, 180)
>> gaussian log files for carbonyl oxygen in my QM target data, right?
>>
>> Wenhao
>>
>> On Wed, Apr 17, 2013 at 1:26 PM, Mayne, Christopher G <
>> cmayne2_at_illinois.edu> wrote:
>>
>>> Carbonyls are a special case in ffTK. The optimal water positioning
>>> in QM is 120 degrees (where the electron density is located. In MM, the
>>> force field uses a point charge model that doesn't account for electronic
>>> structure, hence, the optimal water position is 180 degrees to reduce
>>> steric interaction with adjacent bound atoms. In this special case, ffTK
>>> generates input files for BOTH 120 and 180 degree positioning of waters, as
>>> per the suggestion made either on the CHARMM forums or in the original
>>> CGenFF paper (I don't remember where off the top of my head). This
>>> essentially hedges against errors due to discrepancies between QM and MM
>>> theories.
>>>
>>> Christopher Mayne
>>>
>>> PS Wenhao, we should keep this discussion on-list
>>>
>>> On Apr 17, 2013, at 12:18 PM, Wenhao Liu wrote:
>>>
>>> Chris,
>>> I see your point about charge optimizer. Thanks. So the plugin can
>>> generate more than one acceptor or donor bonding with water molecules for
>>> the atoms in my new molecule(like oxygen) if it can form more than one
>>> bond, right? I think this should be right since I've just tried and find
>>> that the plugin generated three different water bonding structures for the
>>> oxygen in Carboxyl group and that make sense.
>>>
>>> Wenhao
>>>
>>>
>>> On Wed, Apr 17, 2013 at 10:52 AM, Mayne, Christopher G <
>>> cmayne2_at_illinois.edu> wrote:
>>>
>>>> I don't think so. The optimizer judges the ability of a charge set to
>>>> reproduce the interaction, but the positioning of the water is
>>>> predetermined based on geometry, i.e., not a stochastic calculation. The
>>>> best time to modify your weights is when you want to bias the charge sets
>>>> towards getting a particular interaction correct (relative to qm).
>>>>
>>>>
>>>>
>>>> On Apr 17, 2013, at 9:18 AM, "Wenhao Liu" <mdsimulate_at_gmail.com> wrote:
>>>>
>>>> Chris,
>>>> So you mean I can set the weight like to 2 when I deal with
>>>> oxygen-water bonding in the condition that oxygen in my new molecule can
>>>> form two hydrogen bonds with water? Thank you!
>>>>
>>>> Wenhao
>>>>
>>>> 在 2013年4月17日星期三，Mayne, Christopher G 写道：
>>>>
>>>>> It is not required due to the symmetry of water--there is no extra
>>>>> information to be gained by flipping the identities of the hydrogens. ffTK
>>>>> handles the positioning of the water automatically.
>>>>>
>>>>> Regards,
>>>>> Christopher Mayne
>>>>>
>>>>>
>>>>> On Apr 17, 2013, at 1:53 AM, Wenhao Liu wrote:
>>>>>
>>>>> > Hello vmd people,
>>>>> > I was just wondering is it required to set up more than 1 hydrogen
>>>>> bonding for Acceptor (like the oxygen that can bonding with 2 hydrogen of
>>>>> the water) when I need to do the water interaction Gaussian calculation in
>>>>> charge optimization step? But I can only have 1 possible conformation to
>>>>> put water molecule bonding with oxygen in Acceptor indices, the other
>>>>> possible hydrogen boding between oxygen and hydrogen of water should be in
>>>>> different orientation, right? Or I can just set the weight of this
>>>>> calculation to 2 when I do the charge optimization? Thanks in advance.
>>>>> >
>>>>> > Wenhao
>>>>>
>>>>>
>>>
>>>
>>
>>
>
>