On 12/15/09 11:03 PM, Reza Salari wrote:
Thanks for your response.
While I will try that (although it seems it needs quite amount of
scripting), I remember in the past some people in the mailing list
mentioned problems while using nonbond_params directvie with OPLS-AA and
in response it was
I running the simulation of a protein with Fe4s4 cluster. The parameters for
the cluster were obtained from a previously published paper. I have been able
to carry out energy minimization with the following keywords-
;
cpp = /usr/bin/cpp
Dear GMX users,
Hi
I'm working on denaturation of proteins with MARTINI CGFF by Gromacs suit.
according to this paper (J. Chem. Theory and Comput. 2008, 4, 819–834) I
undestand there is a limitation for modeling of folding and unfolding with
MARITI CGFF for systems in which the folding and
Is this a real gromacs-user question?
Have your tried to contact the MArtini developers?
As a matter of fact some of them have prepared a new MARTINI
web-site where a discussion forum will be on.
To answer your question: using MARTINI for the unfolding
mechanism of proteins would be very
subarna thakur wrote:
I running the simulation of a protein with Fe4s4 cluster. The parameters
for the cluster were obtained from a previously published paper. I have
been able to carry out energy minimization with the following keywords-
snip
*a) Can I freeze the movement of the Fe4S4
Hello,
I would like to setup a screensaver to visualize structures as we are
simulating them. We want to avoid slowing down the simulation
significantly. I found a solution that read pdb files. Is there a way
to reduce the frequency mdrun updates the confout.gro?
The structure file (-c) contains
Jack Shultz wrote:
Hello,
I would like to setup a screensaver to visualize structures as we are
simulating them. We want to avoid slowing down the simulation
significantly. I found a solution that read pdb files. Is there a way
to reduce the frequency mdrun updates the confout.gro?
The
Jack Shultz wrote:
Hello,
I would like to setup a screensaver to visualize structures as we are
simulating them. We want to avoid slowing down the simulation
significantly.
Not slowing things down significantly is only going to be possible when
GROMACS can use a processor that isn't going to
Thank you very much Dr Paluch and Dr van der Spoel for your responses.
Then it seems it would be safer to use mixing the combination rules as a last
resort, although it is comforting to know that other people have used
it before successfully.
I think I will look for the parameters that are
Thank you very much. That sounds interesting!
BTW, I finally found out that the only way to use parameters developed using
different combination rules together, is to define them manually in
nonbonding_params section of topology. This sounds a little bit dangerous since
it is sort of mixing
Thank you very much. That sounds interesting!
BTW, I finally found out that the only way to use parameters developed
using different combination rules together, is to define them manually
in nonbonding_params section of topology. This sounds a little bit
dangerous since it is sort of mixing
Hi, I tried energy minimization and I am getting the error while I am
running the minimization step. But then I still tried to carry on with
normal md-simulation, and it was fine, but I am sure it won't give me
the result that it should. Is there a reason for that? I have tried
very low
nishap.pa...@utoronto.ca wrote:
Hi, I tried energy minimization and I am getting the error while I am
running the minimization step. But then I still tried to carry on with
normal md-simulation, and it was fine, but I am sure it won't give me
the result that it should. Is there a reason for
Thanks for your response.
So basically since the Cheatham parameters are using LB rule, I can never use
them with OPLS-AA?
I was thinking if I find the parameters for OPLS atoms that are based on
geometric rule (if there such a thing exists at all), I could use them along
with Cheatham
Hi Justin,
I am trying to plot rdf of one methane molecule in water (spc
water, 1095(water molecule in my file). I did create the file using
genbox (31.010 31.010 31.010). This is the energy minimization file I
am using:
title = Methane in water
cpp = /lib/cpp
nishap.pa...@utoronto.ca wrote:
Hi Justin,
I am trying to plot rdf of one methane molecule in water (spc water,
1095(water molecule in my file). I did create the file using genbox
(31.010 31.010 31.010). This is the energy minimization file I am using:
Surely a 31-nm cubic box is
Hi,
You are right, I had to delete some water molecules, it is working fine now.
Thanks.
-Nisha P
Quoting Justin A. Lemkul jalem...@vt.edu:
nishap.pa...@utoronto.ca wrote:
Hi Justin,
I am trying to plot rdf of one methane molecule in water (spc
water, 1095(water molecule in my
HI,
Okay, so I am trying to plot rdf of one methanol this time in water.
Is there a way to select methanol molecule as a whole (i.e. get rdf
from the center of the molecule), instead of Me, O and H. Even though
I put Me, O and H in same group, I am getting a weird rdf plot
(Attached to
nishap.pa...@utoronto.ca wrote:
HI,
Okay, so I am trying to plot rdf of one methanol this time in water. Is
there a way to select methanol molecule as a whole (i.e. get rdf from
the center of the molecule), instead of Me, O and H. Even though I put
Me, O and H in same group, I am getting
I believe that Justin was suggesting that you move in the opposite
direction than to delete some waters.
The number density for water should be about 32.5 waters per cubic
nanometer, meaning that you should have nearly 1E6 water molecules in
a cubic box with sides of 31 nm, and 1095 water
Jack Shultz wrote:
I guess I misinterpreted the description. I take it there is no built
in mechanism to periodically write the structure.
There is :-) Trajectory output and checkpoint output.
Maybe I could revise
the source code to write the structure at every checkpoint?
Sure. That's
You could also have a script that you optimize for your specific
system that knows the number of frames in the xtc based on the file
size and then trjconv -dump when your .xtc-polling script sees that it
has been updated? Your visualization program could then update based
on the output
Dear all,
I would like to perform MD simulations on a molecule that contains a carbon
chain with a sulfonyl (R-SO2-R) group in between. When looking at the available
atomtypes for ffgmx I didnt find a sulfate S. Only sulfur (S) and DMSO sulphur
atomtypes are available. In literature I did
Niesen, Michiel wrote:
Dear all,
I would like to perform MD simulations on a molecule that contains a
carbon chain with a sulfonyl (R-SO2-R) group in between. When looking at
the available atomtypes for ffgmx I didnt find a sulfate S. Only sulfur
(S) and DMSO sulphur atomtypes are
Thanks for the info.
pb.
On Mon, Dec 14, 2009 at 11:33 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
Pradip Biswas wrote:
Hi,
The atomic numbers of the atom types opls_179 (OS) and opls_180 (OS) are
typed in as 7 in ffoplsaanb.itp instead of 8. Accordingly, while doing QMMM,
these
Hi Jorge,
I'll appreciate if you can send me (biswas...@gmail.com) the following files
if the problem still persists:
1. output.mdrun_em
2. qm_cpmd.log
Also please let me know which version of CPMD you are using.
best,
pb.
On Thu, Nov 19, 2009 at 1:59 PM, jorge_quint...@ciencias.uis.edu.co
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