Thank you both of you (Justin and Albert) sir.
Initially I was using dppc128 and now I changed to POPE 340 and still my
protein (its a GPCR protein) protrude out of the membrane (the same region;
two amino acids).
since you (Justin) you have mentioned that the protein must be completely
inside the
superimpose your receptor PDB files with related structure OPM database
center your lipids in 0 by editconf command in gromacs
then you GPCR would be in the center of the lipids.
PS: 340 lipids is too big for a single GPCR, 140~160 would be enough
before g_membed. You'd better read paper to
On 7/29/13 4:31 AM, pavithrakb wrote:
Thank you both of you (Justin and Albert) sir.
Initially I was using dppc128 and now I changed to POPE 340 and still my
protein (its a GPCR protein) protrude out of the membrane (the same region;
two amino acids).
Out of curiosity, why have you chosen
Files: http://www.sendspace.com/file/vxcnv3
Commands used: http://pastebin.com/raw.php?i=wPqfuUwc
What I want to do: I just want to run the protein without the ligand in
explicit water. Why is the coordinate file not matching topology?
Dear gmx-users,
We currently performed simulations to study the effect of repulsive
electrostatic interactions on the stability of a silk-like protein. The
amino acid sequence of our protein is the following: Lys [ (Gly-Ala)_3 Gly
(Gln or Lys)]_3 where (Gln or Lys) means that we alternatively
On 7/29/13 6:30 AM, Jonathan Saboury wrote:
Files: http://www.sendspace.com/file/vxcnv3
Commands used: http://pastebin.com/raw.php?i=wPqfuUwc
What I want to do: I just want to run the protein without the ligand in
explicit water. Why is the coordinate file not matching topology?
There is lots of stuff. Please look in manual 7.4 and 8, which bring
order to the the morass of available tools.
Mark
On Mon, Jul 29, 2013 at 12:29 AM, jayant james jayant.ja...@gmail.com wrote:
Hi all,
1) I am looking at see if two adjacent helices are changing their
conformation in space.
sir,
the reason for selecting POPE doesn't have much valid reason. I mean, I have
referred previous works and in the recent work they have used POPE membrane
for my protein (the exact protein) simulation. I have searched literature on
selecting a membrane for simulation to know/understand why they
On 7/29/13 9:10 AM, pavithrakb wrote:
sir,
the reason for selecting POPE doesn't have much valid reason. I mean, I have
referred previous works and in the recent work they have used POPE membrane
for my protein (the exact protein) simulation. I have searched literature on
selecting a membrane
Thank you, Justin. I am using gromacs version 4.5.5 and have attached .mdp
file. I followed your advise and pointer to trouble shooting the system
and decomposed the energy to find potential sources for the problem. The
simulation ran for 978 ps, the total energy changed from approximately
The message is perfectly normal. When you do not use all available
cores/hardware threads (seen as CPUs by the OS), to avoid potential
clashes, mdrun does not pin threads (i.e. it lets the OS migrate
threads). On NUMA systems (most multi-CPU machines), this will cause
performance degradation as
Hi,
I am trying to pull/separate a protein dimer by applying constant force in
my SMD. The dimer has dimension 9 x 8 x 5 nm^3, and I'm trying to pull in
the y-direction so I have set the box as 12 x 40 x 8 nm^3. I have also set
my simulation to run for 5 ns. However, after only 251 ps, I got
On 7/29/13 2:12 PM, Scott Pendley wrote:
Thank you, Justin. I am using gromacs version 4.5.5 and have attached .mdp
file. I followed your advise and pointer to trouble shooting the system
The mailing list does not accept attachments. Please either copy and paste its
contents or provide a
On 7/29/13 2:42 PM, kim2811 wrote:
Hi,
I am trying to pull/separate a protein dimer by applying constant force in
my SMD. The dimer has dimension 9 x 8 x 5 nm^3, and I'm trying to pull in
the y-direction so I have set the box as 12 x 40 x 8 nm^3. I have also set
my simulation to run for 5 ns.
Hi all,
I'm trying to compile 4.6.3 on my desktop, but have running into some issues
with FFTW.
Specifically with -DGMX_BUILD_OWN_FFTW=ON make seems to crash with M4 (if I'm
reading it right)
This is not dpkg install-info anymore, but GNU install-info
See the man page for ginstall-info for
Yes, this is a known problem. A race condition with parallel make
exists between the gmxfftw build target and the things that depend on
it. AFAIK, a second call to make will Just Work. There are known ways
for GROMACS to solve this by controlling the dependency properly, but
the leading candidates
I would have made a blunder by selecting the POPE membrane.
But, that paper (one which used POPE for human protein) was published in
ACS-Journal of Chemical Information and Modeling.
I thought following high standard papers are trust worthy.
Thank you so much sir. I will start learning the
Why not do two umbrella sampling simulations: one with initial conformations
from your faster pulling and one with initial conformations from your slower
pulling. Then you can run them both as regular US simulations until (a) neither
US PMF is drifting systematically with increasing simulation
On 7/29/13 9:03 PM, pavithrakb wrote:
I would have made a blunder by selecting the POPE membrane.
But, that paper (one which used POPE for human protein) was published in
ACS-Journal of Chemical Information and Modeling.
I thought following high standard papers are trust worthy.
Thank you so
Hi All,
I am simulating a system in which I have two solid surfaces and I keep them
frozen during simulations. I also exclude the interactions between its
atoms to avoid spurious contribution to the virial pressure due to large
forces between them as suggested in the manual.
I run a nvt for
Thank you so much sir.
the entire thread was highly useful.
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