[gmx-users] simulating large bilayer systems

[Mark Abraham]

Hi,

On Wed, Jan 2, 2019 at 7:53 AM Anuj Ray <anujray107 at gmail.com> wrote:

> Anuj Ray
> 12:07 PM (2 minutes ago)
> to gmx-users
> Sir,
>
> Since the array size of .gro/.pdb file for atom number is not greater than
> 5 digits, that's why if my system has >= 100000 atoms then, it shows that
> no. of coordinates mismatch in .gro and .top file.


It showed a mismatch with a PDB file, because that format has limitations.
If you use a .gro file, then there will be no problem.

Mark

Although the file
> corrected_wat_DMPC_18_32.pdb has 153216 coordinates, i get the following
> error.
>
> Command line:
>   gmx grompp -f minim.mdp -c corrected_wat_DMPC_18_32.pdb -p dmpctopol.top
> -o em.tpr
>
> Fatal error:
> number of coordinates in coordinate file (corrected_wat_DMPC_18_32.pdb,
> 99999)
>              does not match topology (dmpctopol.top, 153216)
>
> Can you please suggest me the solution to this problem ?
>
> Regards
> Anuj Ray
> --
> 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.
>