[gmx-users] Large system

[Ali Ahmed]

Sir
I have done a simulation of 106000 atoms and there was no problem.
Check your number of molecules in your topology and inspect your input file
you will find something wrong. The error says the number of atoms is not
the same in topology and your input.
I suggest using *.gro  rather than pdb which make it easier to check and
inspect the number of atoms and residues and check the top of gro file this
number represents the total number of atoms in your system.

Best

On Wed, Jan 2, 2019 at 12:47 AM Anuj Ray <anujray107 at gmail.com> wrote:

> 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:
>
> > [image: Boxbe] <https://www.boxbe.com/overview> This message is eligible
> > for Automatic Cleanup! (pbuscemi at q.com) Add cleanup rule
> > <
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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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