On 16/01/2018 11:37, ZHANG Cheng wrote:
Hi Justin, thank you very much.
Sorry I still do not fully understand. I have an index file, in which the group
0 is all the residue atoms of the protein, group 1 is the first residue atoms.
I want to calculate the sasa fraction of the residue 1. The
gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc nojump -o trajclust.xtc -n
index.ndx -center
Please read this first:
http://manual.gromacs.org/documentation/2016.1/onlinehelp/gmx-trjconv.html
trjconv is quite powerful, so it worth to know available options.
-Alexandr
On 30/12/2017 16:37, Neha
On 30/12/2017 06:23, Amir Zeb wrote:
Alright Dr. Justin,
Is it kindly possible to get CHARMM-compatible parameters for Mn2+ which
you haven't included in the port?
I'm searching the literature too to find something worthy.
Try to start with following papers:
Hi James,
As a very quick check - did you do any editing of frame_2.gro?
It looks like you have an extra line or removed some line from gro-file.
If you manually edited it, beware of the total count of atoms in the
very beginning of gro-file, which you should edit it as well.
More detailed
Hi Anthony,
Would it work if you take x/y/z components of the distance and subtract
ones extending the size of the box in the corresponding direction?
You will need to extract box size from the *.edr file (unless box is of
fixed size), further use flag -oxyz from gmx distance for xyz
On 27/11/2017 07:21, Ali Ahmed wrote:Hello GMX users
I'm trying to do simulations on multi nodes so I used 8 nodes (128
processors). AS I see there is no difference between 1 node and 8 nodes.
Check the log file showing how many nodes you use, look for a line as in
template:
Running on 2
to define all types in bonded and non-bonded itp.
Thanks,
Rakesh
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On Sun, Nov 26, 2017 at 3:27 PM, Alexandr Nasedkin <nased...@chalmers.se
ll?source=signature=en=rakesh.p...@students.iiserpune.ac.in=22>
On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin <nased...@chalmers.se>
wrote:
Hi,
As I understood the problem, you need to distinguish between surface and
buried carbons?
You could define two atomtypes that diff
Hi,
As I understood the problem, you need to distinguish between surface and
buried carbons?
You could define two atomtypes that differ in name and use it to process
with x2top.
Below is an example of *.n2t lines. You would need to change the charges
and bondlengthes.
...
O OCH
Hi Golnaz,
Try to increase default VdW radius scaling: option -scale in gmx solvate.
If there are large cavities in ICE you may have problem at water
interface though.
Best regards,
Alexandr
On 08/11/2017 15:04, G R wrote:
Hi All,
I’m simulating a box of tip4p ice. when I use the gmx
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