Hi Saman,
You can convert the tpr file to pdb/gro with editconf, and you can convert
(a frame of) the .trr file to gro/pdb with trjconv.
Hope it helps,
Tsjerk
On Sat, Nov 30, 2013 at 8:43 AM, Saman Shahriyari samanshahriy...@yahoo.com
wrote:
Dear users
is there any way to retrieve box
Could anyone please explain the difference between how umbrella and
constaint options in the pulling code work. Based on the manual, I
expect that the only difference
is that umbrella used harmonic potential to bind pulled group to the
reference group (point), while constraint uses shake algorithm
On Sat, Nov 30, 2013 at 1:22 AM, Mahboobeh Eslami
mahboobeh.esl...@yahoo.com wrote:
Thank you for your help
What command do I use to use 8 cores
mdrun -nt 8 -s *.tpr
or
mpirun -np 8 mdrun_mpi -s *.tpr
Chandan
Good luck
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Dear Justin
My system contains lipid bilayer + drug + water molecules.
I want to calculate Potential of mean force as a function of the
distance between the centers of mass of drug and the lipid bilayer.
Based on your suggestion I used pull_geometry = position for my case.
After the
On 11/30/13 9:22 AM, shahab shariati wrote:
Dear Justin
My system contains lipid bilayer + drug + water molecules.
I want to calculate Potential of mean force as a function of the
distance between the centers of mass of drug and the lipid bilayer.
Based on your suggestion I used
On 11/30/13 9:29 AM, jkrie...@mrc-lmb.cam.ac.uk wrote:
As has been asked a number of times before, I have seen minimization halt
at a low number of steps having converged to machine precision when double
precision is not used - does that not mean that double precision is needed
at least for
Dear gmx_users,
My question is about the coulomb LR contribution with PME, I can't access
to david's original post treating this subject in the mailing list (
http://www.gromacs.org/pipermail/gmx-users/2002-May/001455.html) if it
exists, because some links are disabled.If any one can send me the
I might be wrong here, but my expectation is that nowadays you should
not do anything explicitly in this regard. The compensating charge is
automatically applied.
Dr. Vitaly V. Chaban
On Sat, Nov 30, 2013 at 5:14 PM, Benrezkallah Djamila
benrezkal...@gmail.com wrote:
Dear gmx_users,
My
... but not necessarily any good! See
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2012-November/006398.html.
I have seen Gerrit present some convincing results since then, but they do
not seem to be in press, yet.
Neutralizing explicitly seems like the right course just
On 2013-11-30 18:01, Mark Abraham wrote:
... but not necessarily any good! See
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2012-November/006398.html.
I have seen Gerrit present some convincing results since then, but they do
not seem to be in press, yet.
Neutralizing
Sorry to but in on the conversation. Im between computers so cant track it down easy, (on my hard drive) but I did find one older publication comparing gromacs solvent (ion/buffers) effects with plasmon resonance calculated affinities, the results of that single paper showed the closer the
By configuring 8 GT/s PCIE 3.0 for the Nvidia driver, I got a 10% speedup
on Gromacs md_run.
45 ns/day - 50 ns/day (1AKI protein).
This posting is just informational, my findings on how to do this, so
others can possibly also exploit this if they desire so. There is no
question that i'm asking
Dear
GMX Users
I
want to run NVT equilibration and NPT equilibration (after
NVT) for DNA-ligand interaction and want to increase temperature
gradually i.e.
from
0 to 300 K over a 100 ps, but i have some questions about this process:
when
I use simulated anealing in NVT as following
Dear
GMX Users
I
want to run NVT equilibration and NPT equilibration (after
NVT) for DNA-ligand interaction and want to increase temperature
gradually i.e.
from
0 to 300 K over a 100 ps, but i have some questions about this process:
when
I use simulated anealing in NVT as following
annealing_time
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