[gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

[Roja]

Oh my God,i face with wall at beginning as a BEGINNER!!!! ;)))))
I really appreciate you ,sir, for answering my questions patiently,I WILL BACK soon ;)

With regards
Rose

Sent from my iPhone

> On Oct 19, 2017, at 1:14, Alex <nedomacho at gmail.com> wrote:
> 
> No, what I am saying is that you need to meticulously modify the amber99
> forcefield (if that is indeed suitable) to represent your nanosheet. The
> charges have to come from appropriate sources, whether it's your Gaussian
> or whatever. This will fix all forcefield-related errors you are
> encountering. In order to learn about Gromacs forcefield format and how to
> do the editing, please consult the official Gromacs documentation. This
> really needs to be done before you start doing the xyz>pdb conversions, etc.
> 
> The "vacuum gap" is a moot point for MD simulations, especially ones
> involving solvent. Please understand the differences between DFT and
> particle-based simulations. You can put your nanosheet in a bunch of
> different boxes of appropriate size. This forum isn't the right place for
> asking this, I am only replying, because I have experience with using
> Gromacs for things it was never intended. :)
> 
> Best of luck!
> 
> Alex
> 
>> On Wed, Oct 18, 2017 at 3:14 PM, Rose <rose.rhmn93 at gmail.com> wrote:
>> 
>> Oh,you mean that i should make My sheet then just optimize it(with out
>> putting charge) and then convert it to .pdb file and use it in MD as an
>> input? I have checked the literature the suitable FF was amber99.
>> Different question;) , what is the difference between using vaccum gap
>> (that Will be implemented in structure.xyz file) and using smaller box
>> with periodic boundry condition(with out using vaccum gap),are they related
>> to each other at all?!!!
>> Sorry for these childish questions,but I really get confused.
>> 
>> With regards
>> Roja
>> 
>> 
>>> On Oct 19, 2017, at 0:08, Alex <nedomacho at gmail.com> wrote:
>>> 
>>> Hi Rose,
>>> 
>>> It sounds like a lot of things packed in a very short message, so let me
>>> try to clarify a few points:
>>> 
>>> 1. Gromacs is not DFT, it is particle-based. You simulated your nanosheet
>>> in Gaussian and it is my understanding that you used CHELPG to obtain the
>>> partial atomic charges.
>>> 
>>> 2. Those charges in general are not compatible with most MD forcefields
>>> implemented in Gromacs. If I remember correctly, AMBER is the closest to
>>> using CHELPG charges. So, my point is that you need to choose the MD
>>> forcefield properly and set the charges (all non-bonded parameters,
>> really)
>>> accordingly. The same goes for the bonded parameters to represent the
>>> nanomechanical properties of the sheet. This is beyond the scope of this
>>> discussion, as you definitely need to do a thorough literature search and
>>> see what forcefield is appropriate.
>>> 
>>> 3. You ask if your nanosheet is "suitable." Any structure is "suitable"
>> in
>>> principle, as long as the interactions are set properly.
>>> 
>>> It is hard to give any advice beyond that. Simulation of "custom"
>>> structures is a lot of effort. If your system of interest is small, an
>>> alternative to all of this could be DFTMD simulations using CP2K package.
>>> 
>>> Alex
>>> 
>>>> On Wed, Oct 18, 2017 at 1:50 PM, rose rahmani <rose.rhmn93 at gmail.com>
>> wrote:
>>>> 
>>>> first thank you for your attntion, i made ZnS nanosheet with VNL
>>>> software,it has 33 atoms,i choosed vaccum gap,then i optimized and
>> charged
>>>> it with gaussian03,the amino acid is threonin,for the first time i want
>> to
>>>> study the interaction of these two structures, i am not even sure that
>> my
>>>> nano sheet is suitable for this simulation or not,but for the as a
>>>> beginning i prfeer to test it.
>>>> 
>>>> 
>>>> 
>>>>> On Wed, Oct 18, 2017 at 10:48 PM, Alex <nedomacho at gmail.com> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> That would probably depend on the nanosheet material, the particular
>>>> amino
>>>>> acid, the solvent & ionic strength, temperature, etc, etc. But no,
>> there
>>>> is
>>>>> no tutorial and yes, a "nanosheet" can be viewed as a ligand. :)
>>>>> 
>>>>> I don't know if this helps, but could you please first give us an idea
>> of
>>>>> what you're trying to do?
>>>>> 
>>>>> Alex
>>>>> 
>>>>> 
>>>>>> On 10/18/2017 1:09 PM, rose rahmani wrote:
>>>>>> 
>>>>>> Hi
>>>>>> 
>>>>>> I am a beginner user of GROMACS, i want to simulate the interaction of
>>>>>> nano
>>>>>> sheet with amino acid ,but i dont know what should do, how should i
>>>> behave
>>>>>> with these structures ? is there any tutoroial for interaction of nano
>>>>>> sheet and amino acids?
>>>>>> is it like protein-ligand tutorial in GROMACS tutorial?
>>>>>> 
>>>>>> with regards
>>>>>> 
>>>>>> Rose
>>>>> 
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