Hello Ankita
You have to just include the following line in your mdp file
cutoff-scheme=Verlet
And run your grompp with the modfied mdp file to generate tpr file and then
mdrun.
Hope this doesn't give you the same error
On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani
Hi Pavan,
Thank you for your response. I am trying to generate the tpr file with the
following parameter;
; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 25 fs
rlist= 1.0; short-range neighborlist cutoff (in nm)
It might be some typographical errors.
Check the mdp file thoroughly. I think semicolon is required for the last
line in your mdp file
On Mon, Mar 24, 2014 at 5:18 PM, Ankita Naithani
ankitanaith...@gmail.comwrote:
Hi Pavan,
Thank you for your response. I am trying to generate the tpr file
On Mon, Mar 24, 2014 at 12:17 PM, Ankita Naithani
ankitanaith...@gmail.comwrote:
Hi,
I am trying to run a simulation of my protein (monomer ~500 residues). I
had few questions and erors regarding the same.
I have previously run the simulation of the apo form of the same protein
using
On Mon, Mar 24, 2014 at 12:48 PM, Ankita Naithani
ankitanaith...@gmail.comwrote:
Hi Pavan,
Thank you for your response. I am trying to generate the tpr file with the
following parameter;
; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5
On 3/24/14, 7:48 AM, Ankita Naithani wrote:
Hi Pavan,
Thank you for your response. I am trying to generate the tpr file with the
following parameter;
; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 25 fs
rlist= 1.0
On 3/24/14, 7:57 AM, Ankita Naithani wrote:
Hi, so I modified my mdp file which now looks like the following:
title= production MD
; Run parameters
integrator= md; leap-frog algorithm
;nsteps= 2000; 0.005 * 2000 = 10 ps or 100 ns
;nsteps=
The segmentation fault is highly unusual, and suggests that the
installation of gromacs used a shared library that has now
migrated/changed/whatever. I suggest you discuss that with your system
admins and ask them to re-install, or re-run the GROMACS regression tests,
to check things are OK.
Mark
