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 <nedoma...@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.rhm...@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 <nedoma...@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.rhm...@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 <nedoma...@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-requ...@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-requ...@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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.
