Re: [gmx-users] Number of coordinates in .gro file does not match topology

[Ali Ahmed]

Hi,

Check your box size,I had a same problem. I used a larger box then the
problem solved.

Best
Ali

On Mon, Oct 30, 2017 at 6:29 PM, Mark Abraham 
wrote:

> Hi,
>
> How big is the system before and after? Gro format used fixed columns, so
> can sometimes struggle with large systems. Try using .g96 as the output
> file extension
>
> Mark
>
> On Mon, 30 Oct 2017 17:29  wrote:
>
> > Checked the file again. It is the one that gets generated after the
> > solvation command is run.
> >
> > Sent from my iPhone
> >
> > > On 30-Oct-2017, at 9:39 PM, Mark Abraham 
> > wrote:
> > >
> > > Hi,
> > >
> > > The most likely scenario is that you are looking at a gro file that is
> > not
> > > the one that was written by the solvation tool.
> > >
> > > Mark
> > >
> > > On Mon, Oct 30, 2017 at 9:41 AM Aishwarya Smriti <
> > > smritiaishwary...@gmail.com> wrote:
> > >
> > >> Hi!
> > >>
> > >> I'm trying to solvate a system of a CNT and a protein molecule. My
> > updated
> > >> topology file shows 106275 new solvent molecules added but the .gro
> file
> > >> has only coordinates for 6197 new molecules. I'm using SPC model for
> > >> solvating, Please help.
> > >>
> > >> Regards,
> > >> Aishwarya Smriti
> > >> Senior Undergraduate
> > >> Chemical Engineering
> > >> Indian Institute of Technology, Delhi
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> posting!
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> > >>
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Re: [gmx-users] Number of coordinates in .gro file does not match topology

[smritiaishwarya85]

Checked the file again. It is the one that gets generated after the solvation 
command is run.

Sent from my iPhone

> On 30-Oct-2017, at 9:39 PM, Mark Abraham  wrote:
> 
> Hi,
> 
> The most likely scenario is that you are looking at a gro file that is not
> the one that was written by the solvation tool.
> 
> Mark
> 
> On Mon, Oct 30, 2017 at 9:41 AM Aishwarya Smriti <
> smritiaishwary...@gmail.com> wrote:
> 
>> Hi!
>> 
>> I'm trying to solvate a system of a CNT and a protein molecule. My updated
>> topology file shows 106275 new solvent molecules added but the .gro file
>> has only coordinates for 6197 new molecules. I'm using SPC model for
>> solvating, Please help.
>> 
>> Regards,
>> Aishwarya Smriti
>> Senior Undergraduate
>> Chemical Engineering
>> Indian Institute of Technology, Delhi
>> --
>> 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.
>> 
> -- 
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Re: [gmx-users] Number of coordinates in .gro file does not match topology

[Mark Abraham]

Hi,

The most likely scenario is that you are looking at a gro file that is not
the one that was written by the solvation tool.

Mark

On Mon, Oct 30, 2017 at 9:41 AM Aishwarya Smriti <
smritiaishwary...@gmail.com> wrote:

> Hi!
>
> I'm trying to solvate a system of a CNT and a protein molecule. My updated
> topology file shows 106275 new solvent molecules added but the .gro file
> has only coordinates for 6197 new molecules. I'm using SPC model for
> solvating, Please help.
>
> Regards,
> Aishwarya Smriti
> Senior Undergraduate
> Chemical Engineering
> Indian Institute of Technology, Delhi
> --
> 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
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Number of coordinates in .gro file does not match topology

[Vytautas Rakeviius]

You do something wrong. How you solvate?Try something like this:
gmx solvate -cp my_system.gro -cs spc216.gro -o my_system_solv.gro -p topol.top 

On Monday, October 30, 2017, 10:41:31 AM GMT+2, Aishwarya Smriti 
 wrote:  
 
 Hi!

I'm trying to solvate a system of a CNT and a protein molecule. My updated
topology file shows 106275 new solvent molecules added but the .gro file
has only coordinates for 6197 new molecules. I'm using SPC model for
solvating, Please help.

Regards,
Aishwarya Smriti
Senior Undergraduate
Chemical Engineering
Indian Institute of Technology, Delhi
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[gmx-users] Number of coordinates in .gro file does not match topology

[Aishwarya Smriti]

Hi!

I'm trying to solvate a system of a CNT and a protein molecule. My updated
topology file shows 106275 new solvent molecules added but the .gro file
has only coordinates for 6197 new molecules. I'm using SPC model for
solvating, Please help.

Regards,
Aishwarya Smriti
Senior Undergraduate
Chemical Engineering
Indian Institute of Technology, Delhi
-- 
Gromacs Users mailing list

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