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

[Justin Lemkul]

On 10/18/17 5:14 PM, Rose 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.

What Alex is saying is that none of the force fields provided with 
GROMACS has knowledge of ZnS species and you will have to provide all of 
the parameters yourself. If they exist in the literature, then you need 
to implement them. If not, you need to parametrize it from scratch - a 
very advanced and difficult task (if it can even be made to work with a 
classical, pairwise additive functional form). A PDB file without a 
corresponding topology is useless.

-Justin

> 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
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/Support
>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>> -- 
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================