[gmx-users] topology problem with x2top

paul buscemi pbuscemi at q.com
Thu Oct 4 04:53:27 CEST 2018

The procedure you are using is very much like I use.  While I use 54a7 ff you most likely are not but I know the procedure works with oplsaa.ft. 

 In using 54a7ff, I can use ATB to build a small version of the polymer - say 50 atoms or less --. ATB has problems with polymers over  about 300 atoms otherwise you could use their tip directly  . From the generated tip you can obtain the charges and atom types.  I use Avogadro to generate the initial small model and can obtain bond lengths and another estimate of the charges.  You have to be careful to make all of the bond types in the n2t and the bond lengths have to be accurate- grump will complain if these are not close to what it expects - within 10%.

 You probably know this as well, but in my experience  the charges on the full model will hardly ever total to  exactly 0, but they should be less than 0.0001e  on the small model  so the total charge on the full polymer system is less than ~0.1e. with multiple polymers -e.g. a surface.    I’ve found that  PE, PVC, nylon, Me2SiO,  polymer behave well in vacuum and in solvents - despite the fact that -maxwarn 1  and I have had to come to a peaceful settlement for the small charges I usually end up with  ( 0.1e for ~50000 atoms) 

If x2top works with the small model it will work with the full polymer and it’s much easier to flush out the problems with the small model

I’ll see if I can generate the PVDF tomorrow and post the tip and n2t - It will be for 54a7 but maybe it will still provide some insight..

Not sure of how to approach the graphene, but I think Avogadro may have such a model.  Unfortunately Avo does not provide top files.

Paul Buscemi, Ph.D.
Bioinformatics and Computational Chemistry
University of Minnesota.

> On 3,Oct 2018, at 3:32 AM, Maria Luisa <ml.perrotta at itm.cnr.it> wrote:
> Dear users,
> I need help. I want to build the topology of a polymeric chain of PVDF of
> 602 atoms, and of a sheet of Graphene Oxide of 202 atoms. I use the
> version of gromacs 5.1.4. The problem is that it does not recognize some
> atoms in the polymeric chain, and not at all the graphene oxide atoms. I
> already worked with the x2top command, I had already created another
> executable .n2t file, to complete the missing atoms in the atomname file,
> and in the past I built topology for graphene oxide and graphene systems,
> but now, all this command with my previous challenge doesn't t work. I'm
> doing a thousand tests but I do not know how to do it.
> I hope to get help.
> Thank you
> Maria Luisa Perrotta
> Ph.D Student, CNR-ITM
> via P.Bucci, 87036 Rende (Cs)
> Italy
> email: ml.perrotta at itm.cnr.it
> -- 
> 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.

More information about the gromacs.org_gmx-users mailing list