Dear Gmx users,
I had been using Gromacs for couple of years and always found these forums
quite helpful. Right now again I have another question to ask that I was
not able to figure out yet myself and reading previous posts.
I need to the ffG53a6 forcefield to be able to recognize the
Dear all,
I am trying to run simulation with phosphorylated Threonine (TRO) and I
found lot's of info about this issue reading previous posts which explained
on how to patch the force-field files and define this modified amino acid.
After looking at the community forcefield offered here
Thank you Justin for your prompt reply, as usual :)
With the last 2 lines of my previous post, I was referring on how to build
*.itp files for completely new molecules (say lipids such as DMPC, DMPE
or glutathione) that are not defined in the forcefield. I.e. how to derive
dihedral angle code,
Dear gromacs pros,
I need to calculate depth of DMPC bilayer penetration by my 14 aa long
peptide. I'm not sure how to do it, but I have tried g_dist program and
calculated distance between DMPC and peptide groups for every frame of
simulation. Is that correct way of doing it or maybe there is a
Hi Justin,
Sorry I forgot the attachment. Can you see if these files are ok in terms of
sequences and more or less accurately represent both DMPC and DMPE? they
were built in Teilman lab I believe
DMPE: http://sites.google.com/site/kbessonov/dmpe.itp?attredirects=0d=1
DMPC:
Sorry I've just noted that once of the messages made it to the forum, sorry
for repetition.
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DMPE.itp file as attached
[ moleculetype ]
; Name nrexcl
DMPE 3
[ atoms ]
; nrtype resnr residuatomcgnrcharge mass
1 H 1DMPE H1 0 0.4000 1.0080;
qtot:0.36
2 H 1DMPE H2 0
Hello Justin,
You helped me before, and I am grateful for that. So basically my summer
research had ended up with the following results:
I have included my *.ipt files this message is long.
*My question: 1)why once simulation is giving me stable aplha-helix and
other is not if membranes are
I have used do_dssp program to analyze secondary structure during simulation
of DMPC/DMPE. But I am not clear on installation of dssp.
The program seems to work, I have set all the environmental variables so
that dssp binary is seen in /home/DSSP directory, but I am not sure if I
need to download
I was giving today my poster presentation and one of profs from my
department was very critical on the fact that my peptide is drifting or
moving along the DMPC bilayer. Watch video of 100ns simulation here:
He said that is unprobable, I want to know if this is some kind of artifact
(i.e. system
Sorry the link: You see that peptide is moving from right to the left of the
box
http://www.youtube.com/watch?v=_6e4Rfl6Yrc
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Hi Justin,
So after struggling through ... I have confirmed that the error was due to
Gromacs version incompatibility. Now my simulation is past problematic step
and continues running without any error.
Also I am following your advice and also doing the same simulation but with
two equilibration
I think I have not arrived to complete solution of my problem yet, but I
think the cause of early LINCS warnings were version incompatibility. I am
now trying to run simulation on the server that has only 4.0.5 Gromacs, will
see if that helps and whether I will warnings in the middle of
Hello gain Justin,
Now I figured out that the problem was in gromacs version 4.0. So peptide in
water works no problem.
I have used trjconv -pbc mol -ur compact and it solved the artifact problem.
Thanks a lot!
Now I have started simulation on 96 CPU's for 1000ns total run time. But
after 1 day
Hello again,
Thanks for quick replies! I've tried to see what happens if I put peptide
in water and sure enough it failed (uses gromacs 4.0). But when I run it on
machine that I have created the *.tpr file it runs no problem already 5000
steps and the machine uses gromacs 4.0.5.
How could it be
I have written a C++ program that can do it for you in 5 minutes. If you
interested I can send you link to executable.
It counts #of solute molecules and #Na+ and Cl- ions plus DMPC, but I can
adjust it so it can count any number of molecules, I need to know how many
atoms per molecule and it
Hi guys,
I am trying to start simulation on lipid - peptide system, but receive LINCS
warnings of angles rotating more than 30 deg which means that my system is
unstable. I have tried to do mdrun on the DMPC box itself and had no
problems. Once I insert my peptide, the problems starts. I have run
You can try to position your system in Z direction using:
editconf -princ (and bunch of other normal parameters)
Also you can use -rotate parameter to align your system along any axis
Hope it helps
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Thank you Justin,
I have tried to just solvate the peptide in water box using genbox command
and spc216 water
Then I have used the Energy Min mdp file form your tutorial (I have been
folowing your tutorial for couple of days, the difference is that I want to
put my segment on top of the membrane
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