Hi Justin,
Thanks for your reply. I have some follow-up questions. Since the simulation
is high temperature (450 K) there is slight unfolding of the protein.
The box was set up as rhombic dodecahedron with 1.2 nm as the distance
between solute and edge of box.
pdb2gmx -f 1L2Y.pdb -o 1L2Y-proces
You can try a run in implicit solvent to get a feel for the maximum
diameter of the protein while unfolding. You will not have any
certainty unless you can afford a box whose diameter is that of the
straight-line peptide...
Mark
On Sat, Sep 21, 2013 at 1:03 PM, aksharma wrote:
> Hi Justin,
> Tha
Dear Mark and the rest of the Gromacs team,
Thanks a lot for your response. I have been trying to isolate the problem
and have also been in discussion with the support staff. They suggested it
may be a bug in the gromacs code, and I have tried to isolate the problem
more precisely.
Considering th
On Sat, Sep 21, 2013 at 2:45 PM, James wrote:
> Dear Mark and the rest of the Gromacs team,
>
> Thanks a lot for your response. I have been trying to isolate the problem
> and have also been in discussion with the support staff. They suggested it
> may be a bug in the gromacs code, and I have trie
Dear all,
I’m working on some simulations about the adsorption of protein on solid surfaces, which have slab geometry in the x-y plane. In order to reduce the amount of water molecules and at the same time to decrease the unphysical Coulomb interaction between periodic images in the z-direction,
Dear gromacs users
What is the reason of this point that
unit of the emstep (step size)is nm?
I think ps (unit of time) is more resonable.
If I am wrong, please give me explanation about this point.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx
On 9/21/13 1:47 PM, Atila Petrosian wrote:
Dear gromacs users
What is the reason of this point that
unit of the emstep (step size)is nm?
I think ps (unit of time) is more resonable.
If I am wrong, please give me explanation about this point.
Energy minimization is a non-dynamical process;
Dear Justin
Thanks for your reply.
Ok. You are right. There is no "time" during EM.
For example, if I use nstep = 10,000 and emstep = 0.01,
what means of Step size in this case, exactly?
Please give me more explanation.
Best wishes for you.
--
gmx-users mailing listgmx-users@gromacs.org
I am doing this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html
I have set up the randomly placed cyclohexane and water throughout the box.
The problem is when i try the command "grompp -f em.mdp -c biphase.gro -p
cyclohexane.top -o em.tpr" it e
On Sat, Sep 21, 2013 at 9:06 PM, Jonathan Saboury wrote:
> I am doing this tutorial:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html
>
> I have set up the randomly placed cyclohexane and water throughout the box.
> The problem is when i try the command
Dear all
I would like to know the difference between restarting our crashed runs by
1) first generating next.tpr using tpbconv -extend option
then running grompp with this *.tpr file
and finally running mdrun but with no cpi option
2) same as 1 but with -cpi option
3) using only mdrun comma
On 9/21/13 2:47 PM, Atila Petrosian wrote:
Dear Justin
Thanks for your reply.
Ok. You are right. There is no "time" during EM.
For example, if I use nstep = 10,000 and emstep = 0.01,
what means of Step size in this case, exactly?
Please give me more explanation.
A quick Google search tu
On 9/21/13 3:46 PM, Nidhi Katyal wrote:
Dear all
I would like to know the difference between restarting our crashed runs by
1) first generating next.tpr using tpbconv -extend option
then running grompp with this *.tpr file
Why would you run grompp? If you're using it as a source of coor
>Have a look at how Justin's tutorial's .top gets access to a water
topology.
>
>Mark
Thank you very much for the response Mark!
I've looked at his .top and it seems to me that how he included it is by
adding "#include spc.itp". I've added that line to cyclohexane.top before
and after the "#inclu
On 9/21/13 5:15 PM, Jonathan Saboury wrote:
Have a look at how Justin's tutorial's .top gets access to a water
topology.
Mark
Thank you very much for the response Mark!
I've looked at his .top and it seems to me that how he included it is by
adding "#include spc.itp". I've added that line
Dear users,
I was following Justin's tutorial and in the analysis step trjconv was used to
account for any periodicity in the system and then analyses were conducted with
the so-called "corrected" trajectory file.
The first question is: does it means that particles might diffuse though one
sid
On 9/21/13 10:28 PM, Caizk wrote:
Dear users,
I was following Justin's tutorial and in the analysis step trjconv was used to account
for any periodicity in the system and then analyses were conducted with the so-called
"corrected" trajectory file.
The first thing that is important to note
It's the size of the attempted step in conformational space, the distance
from one configuration to the next.
Cheers,
Tsjerk
On Sep 21, 2013 10:11 PM, "Justin Lemkul" wrote:
On 9/21/13 2:47 PM, Atila Petrosian wrote: > > Dear Justin > > Thanks for
your reply. > > Ok. You ...
A quick Google sea
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