Dear gromacs users,
I still have the same problem with the vector convergence. There is a link with
the size of my protein (18 081 atoms) ?
I tried with a small molecule composed with 826 atoms and it seems to work.
Any idea, please.
Best
Esra
Hi,
Hi,
Is Hamiltonian REMD possible with umbrella sampling in pure gromacs 5.1 without
plumed patch ? It should be according to gromacs 5 paper and manual but no
details are provided of how to use it.
If yes, does anyone successfully applied it and could share sample mdp options
used to exchange
On 11/20/15 2:10 AM, surbhi mahajan wrote:
Thankyou sir,
After using g_order -s md_0_1.tpr -f md_0_1.tpr.trr -n sn1.ndx -d z -od
deuter_sn1.xvg
the file order.xvg is created but still my file does not give any
information about the system whether it is in gel phase or liquid phase.
The
Dear Gromacs users,
I wonder whether it is possible to calculate the inertia tensor for the
molecules?
Thank you in advance for the answer
Sten Sarman
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Dear Gromacs User,
Instead of dumping all atoms of a specific type of molecules, I would like to
dump centers of mass (COM) of the molecules during MD simulations in Gromacs to
reduce trajectory storage. I know g_traj can be used to dump COM of molecules
from trajectory files. But, in that
Hi,
Yes, that's a real bug. I'm not yet sure what to do about it, but I'll
continue discussion at http://redmine.gromacs.org/issues/1848
Mark
On Thu, Nov 19, 2015 at 8:06 PM Krzysztof Kuczera wrote:
> Dear Justin and Mark
>
> Thanks for your helpful suggestions.
> Yes, my
On 11/20/15 2:53 PM, S.M. Golam Mortuza wrote:
Dear Gromacs User, Instead of dumping all atoms of a specific type of
molecules, I would like to dump centers of mass (COM) of the molecules during
MD simulations in Gromacs to reduce trajectory storage. I know g_traj can be
used to dump COM of
To whom may have similar problem, that is how I solved it:
First of all, Gromacs by default uses center of mass removal (at least in
versions I use), but that is for 'whole system'. In my case I have a
two-component system and I am interested in collecting density for one of
the components.
So,