Hi,
You can find the file names that it looks for by doing gmx dump -cp
state.cpt.
On 31 July 2018 at 18:55, Eric Smoll wrote:
> Hi Mark,
>
> Thanks for the reply. I do use directories for project management but, up
> until now, I also had a preference for custom filenames. Lesson learned.
>
Take a look at
http://manual.gromacs.org/documentation/2018.2/onlinehelp/selections.html
to learn about the selection syntax in gromacs. There is an example in the
examples section that does precisely what you want.
"com of group 1 plus com of group 2"
This can be used with gmx distance to
In the index editor of make_ndx does "a 1566 1567 1569 1571 1574 1579" not
work? Alternatively, you can just manually make the index file as Sohaib
suggested. An index group is just:
[ name_of_group ]
;atomnr of atoms that make up the group eg.
1566 1567 1569 1571 1574 1579 etc..
On 12 July 2018
What forcefield are you using? Check if CL is defined in your forcefield
(it's probably not, which is why you are getting the error). Each type
under [ molecules ] must have a corresponding [ moleculetype ] section
defined somewhere in your forcefield files.
On 3 July 2018 at 18:47, gangotri dey
On 8 June 2018 at 19:35, Matthew Fisher
wrote:
> Hi there,
>
>
> I'm wondering if anyone could help me. I've been compiling GROMACS in
> Windows using CYGWIN and this tutorial - http://megaddl.pcriot.com/
> installing-gromacs-5-1-1-in-windows-using-cygwin/
>
> However, when I go to make install,
Hi,
I'm doing umbrella sampling and running into the above error. I can't
really increase the box size as that would make the system too big nor can
I use pull-geometry = direction-periodic as I need to use NPT.
But I'm confused on why I get this error in the first place because my
periodic box
1. No, they are written at whatever frequency you specify in your mdp file.
Look at the nstxout, nstvout and nstfout options. You can choose to write
them to the .trr file at each step if you wish.
3. You can use gmx traj -ov -of
On 26 January 2018 at 04:55, Mohd Farid Ismail
Hi,
I'm trying to do an SMD simulation to generate configurations for Umbrella
sampling. I want to pull two groups together.
I'm having trouble understanding why the pulled distance must smaller than
the half the *shortest* box-vector length.
I know that distance is calculated taking
Hi all,
I'm trying to simulate a protein with the CHARMM36 forcefield. I'm using
PME for VdW interactions and since the CHARMM forcefield
uses Lorentz-Berthelot combining rules I set *lj-pme-comb-rule
= Lorentz-Berthelot *in my mdp file. When I try run grompp with the
following command
gmx
