Dear Justin its your conversation regarding pulling of dsDNA.
Because gromacs is replying as there message is too big so cant be send
and due to that I can not replied in orginal conversation.
But I want to start from the last conversation.
from your side
"It seems to me you have two steps to p
Hello Group,
I want to define dihedral potential for a particular
dihedral in GROMACS. My problem is that i have eight sets of parameters
with *different multiplicity (n)* and f*orce constant value (k)* for the
same dihedral of *functional form 1*.
Look around atom 2016, there is a bad contact between the atoms in that
area, hence the infinite force, very high potential energy, and the
minimisation fails.
On Tue, 25 Sep. 2018, 6:48 pm ikjk, <1761440...@qq.com> wrote:
> hello
>I am doing a md with martini force filed,I create a box, ther
Hi,
That looks like some kind of bug in mindist. Does an earlier version work
for you? Are you able to upload a report for us at
https://redmine.gromacs.org?
Thanks
Mark
On Tue, Sep 25, 2018 at 3:30 PM ABEL Stephane wrote:
> Hi All,
>
> I would like to use g_mindist (vGMX2018.2) to compute th
Hello everyone
I use Gromacs 18.3. when I use the command "gmx pdb2gmx -f protein.pdb -o
protein.gro" it makes a topology file. But this topology haven't
"posre_Chain _A.itp" or any other posre in part "; Include chain topologies"
im confused, that what is wrong?!
Do I can add this posre parts into
Hi All,
I would like to use g_mindist (vGMX2018.2) to compute the number of total
contacts between each residue of a protein and surfactant molecules. For this I
use the following command
gmx_mpi mindist -f myXTC.xtc -s MYPDB.pdb -n MYNDX.ndx -b 20 -e 215000 -dt
4 -d 0.4 -respertime -prin
Hi,
For such specific questions, it will be better to directly contact the authors
of that study. Since the paper is not too long ago yet, they might share their
input files with you.
Good luck,
Gerrit
Dear all, I'm doing the QMMM simulation about OH radicals interacting
with DNA's
Dear all, I'm doing the QMMM simulation about OH radicals interacting
with DNA's base (Guanine) by using GMX-CPMD package. Based on the paper
"Multiscale QM/MM Molecular Dynamics Study on the First Steps of Guanine Damage
by Free Hydroxyl Radicals in Solution (web site:
https://www.ncbi.n
hello
I am doing a md with martini force filed,I create a box, there is a double
monolayer, then I solvate it, but when I did energy minimization,
gmx grompp -f minim.mdp -c solv.gro -p dppc.top -o em.tpr then
NOTE 1 [file minim.mdp]:
With Verlet l
Dear all, I'm doing the QMMM simulation about OH radicals interacting
with DNA's base (Guanine) by using GMX-CPMD package. Based on the paper
"Multiscale QM/MM Molecular Dynamics Study on the First Steps of Guanine Damage
by Free Hydroxyl Radicals in Solution (web site:
https://www.ncbi
by using only the .gro is it possible to calculate the secondary
structure of protein.because when i am using this comment
do_dssp -s aa_charmm-eq.gro -n ../index-p.ndx -sss scount-p-0-1.xvg -o
ss-p-0-1.xpm
the error is
Can not open file:
traj.xtc
because i have the all atom gro file (obtained by c
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