[gmx-users] Large system

[Anuj Ray]

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. 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)








On Wed, Jan 2, 2019 at 12:18 AM <pbuscemi at q.com> wrote:

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> As suggested,  compare the number of molecules/atoms implied in your top
> file against that in your gro/pdb file.  This is one aspect of Gromacs that
> it never gets wrong.
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Bratin
> Kumar Das
> Sent: Tuesday, January 01, 2019 5:22 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Large system
>
> There must be something wrong in your pdb or gro file. Give the proper
> error
> message. They way you told your problem..no one can understand.
>
> On 01-Jan-2019 11:41 AM, "Anuj Ray" <anujray107 at gmail.com> wrote:
>
> Respected Sir
>
> I am trying to prepare a minimization input file (.tpr) for a system having
> 153216 atoms but the grompp command is reading only upto 99999 atoms. What
> is the procedure to prepare the input for such system?
>
> Regards
> Anuj
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