> I run the same mdp files for glucose in vaccum.
>
> I ma geting the proper results, I can visualize the strucutre properly in
> VMD.
>
> If I use same for water why I am not geting proper structure ?
>
> Nilesh
Observe the evolution of energy for your water, after all.
--
Dr. Vitaly V. Chaba
Nilesh Dhumal wrote:
I run the same mdp files for glucose in vaccum.
I ma geting the proper results, I can visualize the strucutre properly in
VMD.
If I use same for water why I am not geting proper structure ?
You're comparing dissimilar systems and expecting them to somehow behave the
s
I run the same mdp files for glucose in vaccum.
I ma geting the proper results, I can visualize the strucutre properly in
VMD.
If I use same for water why I am not geting proper structure ?
Nilesh
On Fri, May 20, 2011 9:48 am, Erik Marklund wrote:
> Exactly. So now is the time for skillful scri
Exactly. So now is the time for skillful scripting.
Erik
Nilesh Dhumal skrev 2011-05-20 15.31:
I used the same topology file to run 256 water molecules simulation and I
got the proper result (compared with reported one).
The problem is to visualize the trajectory in VMD since gromacs fails t
I used the same topology file to run 256 water molecules simulation and I
got the proper result (compared with reported one).
The problem is to visualize the trajectory in VMD since gromacs fails to
write valid pdb files when the coordinates are too large.
Nilesh
On Fri, May 20, 2011 5:22 am,
Justin A. Lemkul skrev 2011-05-19 22.42:
Vitaly Chaban wrote:
For vacuum systems, "pbc = no" in conjunction with zero cutoffs is
correct
to obtain a gas-phase system.
For reasonably large box, this is the same heck.
Setting a box size and using "pbc = xyz" precludes the use of infinite
Vitaly Chaban wrote:
For vacuum systems, "pbc = no" in conjunction with zero cutoffs is correct
to obtain a gas-phase system.
For reasonably large box, this is the same heck.
Setting a box size and using "pbc = xyz" precludes the use of infinite cutoffs,
which should be the most rigorous
Very good.
Have you take a moment to define the box in the GRO file?
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
On Thu, May 19, 2011 at 4:05 PM, Nilesh Dhumal wrote:
> if I set pbc=xyz in energy minimization mdp file then I get
>
> For vacuum systems, "pbc = no" in conjunction with zero cutoffs is correct
> to obtain a gas-phase system.
For reasonably large box, this is the same heck.
Nilesh: visualize your system, using VMD or ngmx. The behavior of your
molecular cluster during the first ps will provide an answer. Are
Vitaly Chaban wrote:
the equlibration file I used
title = cpeptid position restraining
cpp = /usr/bin/cpp
constraints = none
integrator = md
dt = 0.001; ps !
nsteps = 100 ; total 1.0 ps.
nstcomm
if I set pbc=xyz in energy minimization mdp file then I get following error
ERROR: can only have neighborlist cut-off zero (=infinite)
with coulombtype = Cut-off or coulombtype = User and simple neighborsearch
without periodic boundary conditions (pbc = no) and
rcoulomb and rvdw set to zero
ERRO
> the equlibration file I used
>
> title = cpeptid position restraining
> cpp = /usr/bin/cpp
> constraints = none
> integrator = md
> dt = 0.001 ; ps !
> nsteps = 100 ; total 1.0 ps.
> nstcomm
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