VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Tue May 05 2015 - 09:41:16 CDT

Davide,

You can assume that for this particular orientation of water, along this particular interaction vector that there is no minimum; if there is no minimum, we usually discard that specific target data.

With regards to your second question, the optimization is specific to the water+molecule; you are optimizing this interaction after all. In addition to these input files, ffTK will write three additional input files for single point energy calculations (not optimizations):
1) single point energy calculation for water at HF/6031G*
2) single point energy calculation for molecule at HF/6-31G*
3) single point energy calculation for molecule at MP2/6-31G*

Regards,
Christopher Mayne

On May 5, 2015, at 3:48 AM, Michetti Davide wrote:

> Dear Christopher,
>
> If the water keep escaping can I assume that there is no interaction and avoid the point or should I consider it an error? Another problem that I have encountered is that when I write the gau input files, in the water interaction step, I do not get automatic input files for the separate optimization of water and my molecule. For what I understood from the tutorial and the article, they should be automatically generated, shouldn´t they?
>
> Regards,
>
> Davide
>
> On 4, May, 2015, at 18:38 PM, Mayne, Christopher G <cmayne2_at_illinois.edu> wrote:
>
>> Davide,
>>
>> Optimized water positions far form the interaction site are indicative of no energy minimum for the specified interaction. Double check that you have properly assigned the water orientation (donor vs acceptor) and inspect the input files to ensure that ffTK has properly positioned the water molecule(s). In some cases, the water interaction profile is strongly perturbed by the local environment, e.g., adjacent atoms. I don't have a lot of experience working with charged species, but I can imagine this will affect the interaction profile.
>>
>> Regards,
>> Christopher Mayne
>>
>>
>>
>>
>> On May 4, 2015, at 8:49 AM, Michetti Davide wrote:
>>
>>> Hei,
>>>
>>> I am following the FFTK tutorial to parametrize an Uracilate anion (negative charge on N1). Looking at the optimization of some donor water, in the water interaction step, I have seen that the one that are interacting with C2, C4, C5 and H5, H6 move really far from the molecule. Is it normal or have I messed up with the setup?
>>>
>>> Best,
>>>
>>> Davide
>>>
>>
>
>