Thank you so much for your time and explanation.
I am recalculating the energy co-ordinates and using it in g_lie
calculations.
I have read the manual and changed the .mdp file I am using. The following
is the mdp file, please check for the correctness. The text in bold font are
newly included af
Thanks for that explanation.
I would like to know this with little more detail. What do you mean by RF-0
and which cut-off value are you talking about?
Rerunning the trajectory means the whole MD run again?
Thanks.
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Dear Tom,
The explanation really helps me understand LIE much more clearer.
What's the issue if I have used PME coulombtype? I have actually used PME.
Thanks,
Peterson J
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Sent fr
Hello everyone,
I have a doubt about LIE calculation using g_lie in gromacs. This doubt is
about the values automatically assigned for -Clj and -Cqq flags when I ran
the following command:
$ g_lie -f J32_md10ns.edr -o LIE_1A1_J32.xvg -b 7001 -e 1 -ligand J32
The following text contains my op
Thank you so much for clearing my doubt.
I have another doubt that how can I use g_fg2cg program in reverse
transformation (RT) while this program is not an internal GROMACS program.
The RT tutorial in MARTINI website says that one has to compile and source
the files from rev_trans.tar.gz.
How d
Dear Jan,
Thanks for the link. The tutorials available here are very helpful start
preparing the systems for simulation but would like to know how to merge the
custom version of Gromacs for CG available in Martini web site with my
existing Gromacs installation.
Moreover how to make use of all the
Dear Gromacs Users,
I would like to know if there are any tutorials for Coarse-Grained MD
Simulation available anywhere.
Thanks
Peterson J
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Dear colleagues,
I have some doubts about LIE and would like some clarifications.
While I calculate the LIE using g_lie, it gives the DGbind energy in KJ/mol
and a standard deviation in parentheses. How well can I use this value alone
or meaningful it is by itself in comparing the binding affinit
Dear colleagues,
Thanks for opening up this topic. I also have some doubts about LIE and
would like some clarifications.
While I calculate the LIE using g_lie, it gives the DGbind energy in KJ/mol
and a standard deviation in parentheses. How well can we use this value
alone or meaningful it is by
Hi Justin, Thanks for that information.
I also would like to confirm with you that should I combine my metal ion too
while I combine Protein and POPC into Protein_POPC group to be used in COMM
removal? So that I will have a group Protein_HEM_POPC.
Thanks
Peterson J
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Hi,
Did you call your genrestr output in your mdp file using define = * ? (for
example define = -DPOSRES ; where posres was your file name.)
Thanks
Peterson J
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Thanks for that comment.
I've another query during inflating step in Justin's tutorial.
In my case, during the inflation, 4 lipids from the upper and 2 lipids from
the lower leaflets were removed.
Would there be a problem in this sort non-uniform deletion (I mean like 4
from upper and 4 from lowe
Hi Justin,
That works really fine and thanks.
Now, how can I add additional SOL molecules only one side of the bilayer
(either upper or lower)? Since my protein binds at the outer side
(extracellular region) of the membrane I can only fill the upper
(extracellular) region with SOL molecules inste
Thank you so much for that, Justin.
Now I could expand the bilayer.
I've another query. My protein has a small N-terminal portion embedded in
the membrane, I would like to insert only this part into the membrane during
'packing the lipid around the protein' step in your tutorial. Initially I
was
Hi Justin,
Thanks for all your help to get me through membrane simulations.
I've a problem to be solved. I need a long and thick membrane to simulate a
big protein. The longest bilayer that I can download from Tieleman's website
is 64 molecules long.
How can I make (double or triple the bilayer)
Hi Justin,
I have the following Notes during NPT equilibration.
NOTE 1 [file pr_NPT.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file pr_NPT.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
Wh
Thanks Justin,
The explanations are very very useful during my course of simulating a
protein with POPC.
I also would like to get explanation on how to simulate a protein which has
only its N-terminal region embedded in the membrane but the rest in solvent.
What is the easy and accurate way to d
Hi Justin,
I have another doubt on the strong posres that was included in the topology
file. When do we need to remove that position restraint? Does it really
affect at point of time the system?
Thanks
Peterson J
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Thanks for the comment. By the way how to make a bigger box at this time of
the tutorial without affecting any part of the system. Can I use editconf
with slightly bigger number for z-axis (something like 6.7 which was 5.7
before)?
Thanks
Peterson J
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Hi Justin,
I followed your comments and now at the stage of adding solvents.
I wonder to see the protein after shrinking step to have no SOL molecules as
there were SOL molecules in the source popc128b.pdb. Had we removed all the
original SOL molecules anywhere during the course of tutorial?
I al
Hi Justin,
Thanks for the suggestion I got it solved somehow. The main problem was in
the popc128b.pdb itself, it has first 64 lipids and half of the SOl
molecules followed by rest of the POPC and SOL molecules. When I rearranged
them the error was solved.
But now another thing I would like to c
Hi Justin,
Thanks for the effort to help me.
I still no out of the error. The following is the content of my
topol_popc.top
; Include chain topologies
#include "gromos53a6_lipid.ff/forcefield.itp"
#include "popc.itp"
; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"
; Include io
Hi Justin and Anirban,
I started a membrane simulation with POPC bilayer after a training with the
given KALP peptide and DPPC bilayer. I am following both of your tutorials
(mainly the Justin's). I have problem at where I generate a .tpr file for a
DPPC (POPC here)-only system using grompp.
I se
Dear GROMACS Users,
I'm planning to work on a protein that activates itself under lower pH
conditions. And I don't have any clues how to do it in GROMACS. My first
question is about the possibilities to do this in GROMACS, has anyone done
this before? It can even be a constant simulations at a par
Dear colleagues,
Has anyone run simulation with heme moiety in GROMACS with AMBER FF before?
I have a problem running it. I need the topology parameters for the heme.
Thanks
Peterson
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Zhang Bing,
I guess it is problem in your visualizers. Try to label the atom using VMD
which goes well with most of the file types derived in GROMACS. I hope
you'll see the atom as FE not just F.
Thanks
Peterson
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