Thank you very much.
Trjconv works fine.
Marian
On Mon, Mar 9, 2009 at 1:10 PM, Justin A. Lemkul wrote:
>
>
> Mark Abraham wrote:
>
>> - Original Message -
>> From: Nuno Azoia
>> Date: Monday, March 9, 2009 21:52
>> Subject: Re: [gmx-users] ed
raham wrote:
> > - Original Message -
> > From: Nuno Azoia
> > Date: Monday, March 9, 2009 21:52
> > Subject: Re: [gmx-users] editconf and genbox using method
> > To: Discussion list for GROMACS users
> >
> >> Hello!
> >>
> >> Your box
Mark Abraham wrote:
- Original Message -
From: Nuno Azoia
Date: Monday, March 9, 2009 21:52
Subject: Re: [gmx-users] editconf and genbox using method
To: Discussion list for GROMACS users
Hello!
Your box isn't rectangular. Your problem is just VMD display the gro
file w
- Original Message -
From: Nuno Azoia
Date: Monday, March 9, 2009 21:52
Subject: Re: [gmx-users] editconf and genbox using method
To: Discussion list for GROMACS users
> Hello!
>
> Your box isn't rectangular. Your problem is just VMD display the gro
> file with a rect
Hello!
Your box isn't rectangular. Your problem is just VMD display the gro
file with a rectangular shape. If you need to see your system properly
try to transform your .gro file in a .pdb file first, using trjconv.
Try trjconv -h to see the options
Nuno Azoia
On Mon, 2009-03-09 at 12:23 +0200,
- Original Message -
From: Marian Butu
Date: Monday, March 9, 2009 21:24
Subject: [gmx-users] editconf and genbox using method
To: gmx-users@gromacs.org
> editconf -f pep1 -o -bt octahedron -d 0.3 -c
This command line should provoke some warnings at least. Have a look at them,
an
Hi,
I want to obtain a dodecahedron box to start a simulation of a small
peptide. But, even if I use dodecahedron option or octahedron, I obtain a
rectangular box.
Gromacs version: 4.0.4 compiled on redhat server 5 (I do this after 3.2.1
binaries for MS Windows)
Command line that I used:
pd
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