Re: [gmx-users] PBC ISSUES IN GROMACS

[Mark Abraham]

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
had useful information

Mark

On Mon, 14 Aug 2017 09:17 Neha Gupta  wrote:

> Hi gromacs users,
>
> After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc
>
> However, in the movie file, I witnessed bizarre long bonds...
>
> How to fix it?
>
> Any suggestions please?
>
>
> Thanks,
> Neha
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Re: [gmx-users] PBC ISSUES IN GROMACS

[David van der Spoel]

On 14/08/17 09:17, Neha Gupta wrote:

Hi gromacs users,

After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc

However, in the movie file, I witnessed bizarre long bonds...

How to fix it?

Any suggestions please?

trjconv -pbc whole



Thanks,
Neha




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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[gmx-users] PBC ISSUES IN GROMACS

[Neha Gupta]

Hi gromacs users,

After simulation for 5 ns, I generated a movie.pdb file using .gro and .xtc

However, in the movie file, I witnessed bizarre long bonds...

How to fix it?

Any suggestions please?


Thanks,
Neha
-- 
Gromacs Users mailing list

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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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