Dear All!
I'd like to perform several simulations of the membrane protein
started from the common conditions which differs only in the initial
velocities ( for each simulation random speed distribution will be
used from the Maxwell distribution).
Because I simulate membrane protein the long
If the system is already well equilibrated previously then you can probably
safely reassign velocities during NPT. The best way to do this would probably
be to take the equilibrated checkpoint file as the starting point:
grompp -f genvel-yes-npt.mdp -t previous.cpt ...
You'll still have to wait
Dear all,
My system contains lipids, protein and water.
I want to energy minimize it, so ran grompp:
# grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
and then:
# mdrun -v -deffnm em
The output is:
Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps
Dear All,
I just run a grompp command grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p
topol.top -o npt.tpr. It gives the following message,
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
On 9/29/12 3:08 AM, Peter C. Lai wrote:
If the system is already well equilibrated previously then you can probably
safely reassign velocities during NPT. The best way to do this would probably
be to take the equilibrated checkpoint file as the starting point:
grompp -f genvel-yes-npt.mdp -t
On 9/29/12 3:19 AM, Shima Arasteh wrote:
Dear all,
My system contains lipids, protein and water.
I want to energy minimize it, so ran grompp:
# grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
and then:
# mdrun -v -deffnm em
The output is:
Steepest Descents:
Tolerance
Hi,
There's a plugin in VMD called volmap which I think can be used for this
kind of analysis.
Bharat
On Sat, Sep 29, 2012 at 9:27 PM, rama david ramadavidgr...@gmail.comwrote:
Hi Gromacs Users,
I did simulation of two random coil peptides for 100ns.
Peter, Justin,
Thanks alot for the comments.
In the current work I do short simulation of the membrane receptors (
100 ns) started from different conformations of that proteins in the
common physical conditions and than do Essential Dynamics analysis of
the calculated trajectories and compare
On 9/29/12 8:47 AM, James Starlight wrote:
Peter, Justin,
Thanks alot for the comments.
In the current work I do short simulation of the membrane receptors (
100 ns) started from different conformations of that proteins in the
common physical conditions and than do Essential Dynamics
On 9/29/12 12:55 PM, Ali Alizadeh wrote:
Dear All users
I have a system with 3 layers,
when i run grompp program, encounter with this error.
First and 3th layer is the same, and middle layer is water. what's
this error about?
grompp is looking for some group called 1 (the number one) but it
On 9/29/12 3:02 PM, Ali Alizadeh wrote:
Dear All users
make_ndx
How to i can create a my especial index file?
Is there a tutorial related to it?
http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx
Also, typing help at the prompt when running make_ndx provides examples and
Dear Hovakim
Actually it is possible that the ethidium bromide is
indeed intercalating in the DNA, because this is
expected to happen (experimentally) but if you really
see the intercalation, it could be just luck. The time
scale needed, in order that such even happens in
classical molecular
Dear All,
for my original MD, based on mdp file the total time is 500 ps. After it
finished, I have decided to extend the MD run to 2.5 ns.
I think the following command should be used:
tpbconv -s original500ps.tpr -extend 2000 -o md-0.5ns-to-2.5ns.tpr
But as for in the original mdp file
Dear all,
I am trying to minimize the energy of a polymer system I have. I have
successfully modified the n2t file to include force fields for atoms that were
not present. However now I am using grompp before using mdrun (to minimize).
However I have a question should the .ITP and .RTP files
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