hey thanks Mark
What do you mean by -the random seed is in a different variable.Can you
please explain the random seed
On Fri, May 3, 2013 at 1:32 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
gen_vel controls the generation of random velocities. grompp follows it
(but I'd have to
Hi all,
My simulation is composed of 2 protein chains wrapped around a lipid disk
composed of a dozen different lipid types, water and ions in a 15nm cube.
The protein encircles the mixed composition lipid disk.
I've got 4 duplicate simulations with velocities generated from a different
random
Then there is a wealth of papers that describe secondary structure
determination from the experimental point of view that you should look for.
NMR and CD would be the first obvious methods that come to mind, but there are
probably others as well.
These should be able to help you validate or
Dear All,
I want to calculate water and ions density around polymer. After MD I see
my polymer goes near the edges of box and rather some part is out of box.
So in order to calculate water and ion density I think polymer should be
near the center of box (please correct me if wrong)
So by doing
Sorry forgot to add:::
by doing this I can see my polymer near the center of box
On Mon, May 6, 2013 at 11:21 AM, gromacs query gromacsqu...@gmail.comwrote:
Dear All,
I want to calculate water and ions density around polymer. After MD I see
my polymer goes near the edges of box and rather
On 5/6/13 4:21 AM, gromacs query wrote:
Dear All,
I want to calculate water and ions density around polymer. After MD I see
my polymer goes near the edges of box and rather some part is out of box.
So in order to calculate water and ion density I think polymer should be
near the center of box
hai
i would like to use Reax force field,can we use reax force field
in gromacs and if any one please tell to me weather reax ff is useful for
protein
--
regards
M.SathishKumar
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I want to do simulation of protein at pH 12, in this case experimentally
reported that the disulphide bonds of protein was broken and sulphurs
become S negative . Can you please tell me making of disulphide as S- and
S- is it correct and how to set force field to this.
I really don't think thats possible at the moment. All interactions in Reax, if
I recall correctly, are dependent on bond order, which is not an implemented
concept in gromacs.
Erik
On 6 May 2013, at 12:51, Sathish Kumar sathishk...@gmail.com wrote:
hai
i would like to use Reax
On 5/6/13 6:51 AM, Sathish Kumar wrote:
hai
i would like to use Reax force field,can we use reax force field
in gromacs and if any one please tell to me weather reax ff is useful for
protein
It won't be easy to use Reax, if it's even possible. You would have to make
some serious
On 5/6/13 7:03 AM, Sathish Kumar wrote:
I want to do simulation of protein at pH 12, in this case experimentally
reported that the disulphide bonds of protein was broken and sulphurs
become S negative . Can you please tell me making of disulphide as S- and
S- is it correct and how to set
Dear Justin,
You don't need to change the trajectory in any way to do density
measurements
I read sometime before in some paper: water density falls around polymer
(COM) at a distance nearly 4.5nm when it is in box of 10x10x10 nm. I assume
the polymer must be near the center of box so 5nm on
Thank you sir
On Mon, May 6, 2013 at 4:39 PM, Justin Lemkul jalem...@vt.edu wrote:
On 5/6/13 7:03 AM, Sathish Kumar wrote:
I want to do simulation of protein at pH 12, in this case experimentally
reported that the disulphide bonds of protein was broken and sulphurs
become S negative .
Thank you sir
On Mon, May 6, 2013 at 4:38 PM, Justin Lemkul jalem...@vt.edu wrote:
On 5/6/13 6:51 AM, Sathish Kumar wrote:
hai
i would like to use Reax force field,can we use reax force field
in gromacs and if any one please tell to me weather reax ff is useful for
protein
I want to do simulation of protein at pH 12 so i have to deprotanate
tyrosine,tryphtophan.Can you please tell me how i can do with pdb2gmx
command
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regards
M.SathishKumar
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On 5/6/13 7:32 AM, gromacs query wrote:
Dear Justin,
You don't need to change the trajectory in any way to do density
measurements
I read sometime before in some paper: water density falls around polymer
(COM) at a distance nearly 4.5nm when it is in box of 10x10x10 nm. I assume
the
Please use informative subject lines. No subject often gets flagged as spam,
and thus people who may be able to help you may never see your message.
On 5/6/13 7:58 AM, Sathish Kumar wrote:
I want to do simulation of protein at pH 12 so i have to deprotanate
tyrosine,tryphtophan.Can you
Hi all,
I am trying to preform oscillatory shear flow on Gromacs. Is there any existing
commands/codes to do it or do I have to modify the code myself? If I have to
modify code, where can I find the source code for deform?
Thank you so much!
Shirley Young
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gmx-users mailing list
Hello,
I have successfully generated a 945MB mtx hessian storing the normal modes
of a ~1500AA protein using mdrun with the nm integrator and no cutoffs.
However, when I try to analyze the normal modes and create trajectories
using g_nmeig, I can't seem to generate any output. I am running
On 5/6/13 2:16 PM, Bryan Roessler wrote:
Hello,
I have successfully generated a 945MB mtx hessian storing the normal modes
of a ~1500AA protein using mdrun with the nm integrator and no cutoffs.
However, when I try to analyze the normal modes and create trajectories
using g_nmeig, I can't
On Mon, May 6, 2013 at 3:48 AM, Kong xq xqkong...@gmail.com wrote:
Hi Mark,
Thanks for your great help. I am sorry for the negligence to state the
variation value correctly( it should be 0.011 rather than 0.11). Does this
somewhat small value indicate the generalized equilibrium achieved?
Hi all
I am doing an NVE simulation of a protein immersed in water, and I want
to keep track of the potential energy in the protein. Do you know how can I do
it?.
I tried saving the energy of the protein ( the protein as an energy group) in
the .edr file, but when I checked the file with
On 5/6/13 5:58 PM, jhon michael espinosa duran wrote:
Hi all
I am doing an NVE simulation of a protein immersed in water, and I want
to keep track of the potential energy in the protein. Do you know how can I do
it?.
I tried saving the energy of the protein ( the protein as an energy
Hi Justin
Thanks for your answer.
Actually, you are right and that is what I am doing now, but it is really
time consuming and it is like
double calculating because the potential energy is computed during the MD.
Any way thanks
John Michael
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Dear Stephan,
thank you for your reply.
I'm performing some test with antechamber for a de-novo parametrization,
hope to see some good results with it.
You probably have to do a hand job. Look at the .itp/top files and then
the force field parmeters, here's not many atoms, so it would take
Chris, not entirely sure if would work, but what about set of particles located
at the center of the bilayer (might require anchoring/freezing) which only
interacts (via repulsion only) with water, and setting the interaction such
that it manages to exclude it from the bilayer region you
Hi,
I am running mdrun-gpu on Gromacs 4.5.5 (with OpenMM). This is my first
time using a GPU. I get the following error message when attempting to run
mdrun-gpu with my .tpr file:
---
Program mdrun-gpu, VERSION 4.5.5
Source code file:
Hi Chris,
Just think of another possible way without modifying the code. The task can be
achieved by increasing the LJ repulsion term between the lipid tail atoms and
water molecules, but keeping all other interactions unchanged. To do so, the
free energy code can be used. You can create a
Hello Justin sir
In your tutorial file for umbrella sampling for Aβ42 protofibril, what was
the criteria used to determine the coordinates of center of mass and box
size which you have takes as
editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box
6.560 4.362 12
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Thanking
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