Thanks. I am definitely going to look into that.
Quoting chris.ne...@utoronto.ca:
Nisha:
Simply applying available tools and seeing if the distribution looks
okay is not a good plan. You should have a very well-defined idea of
what you are trying to test and then pick a tool to get that done.
Nisha:
Simply applying available tools and seeing if the distribution looks
okay is not a good plan. You should have a very well-defined idea of
what you are trying to test and then pick a tool to get that done.
For example, perhaps you have a reference that provides the converged
distrib
nishap.pa...@utoronto.ca wrote:
Well I guess, what I am trying to get at is, for my system I want to
make sure that 100ns has covered all the conformational changes within
the molecule, although I know there is not that much conformational
changes for glycine molecule, but I just wanted to co
Well I guess, what I am trying to get at is, for my system I want to
make sure that 100ns has covered all the conformational changes within
the molecule, although I know there is not that much conformational
changes for glycine molecule, but I just wanted to confirm. I did run
g_angle comma
nishap.pa...@utoronto.ca wrote:
So is there a way I can test for convergence for my zwitterion for 100ns
run?
I'm not yet clear what you're assessing or how you define convergence. In
addition to what Chris said, you can look at dihedral transitions with g_angle.
Surely there are a few
So is there a way I can test for convergence for my zwitterion for 100ns run?
Quoting "Justin A. Lemkul" :
nishap.pa...@utoronto.ca wrote:
Okay so I tried to analyze the torsion using g_chi and g_rama for
one glycine zwitterion in water. for g_rama I didn't see anything
in xmgrace, and
nishap.pa...@utoronto.ca wrote:
Okay so I tried to analyze the torsion using g_chi and g_rama for one
glycine zwitterion in water. for g_rama I didn't see anything in
xmgrace, and same for g_chi. I used this command for g_chi
g_chi -f traj.xtc -s gly.gro -phi -psi
When I run the command it
Okay so I tried to analyze the torsion using g_chi and g_rama for one
glycine zwitterion in water. for g_rama I didn't see anything in
xmgrace, and same for g_chi. I used this command for g_chi
g_chi -f traj.xtc -s gly.gro -phi -psi
When I run the command it says 1 residue with dihedrals fou
Nisha,
The approach is dictated by the goal. What do you want from this? and
why are you doing it? e.g. if you want to test the FF, then it is a
good idea to at least include US as a part of your strategy; if you
want to determine if 100 ns of equilibrium sampling is sufficient to
converg
Da: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] per conto di
nishap.pa...@utoronto.ca [nishap.pa...@utoronto.ca]
Inviato: venerdì 6 agosto 2010 17.08
A: gmx-users@gromacs.org
Oggetto: [gmx-users] Conformational sampling
Hello,
I would
Hello,
I would like to do conformational sampling for my simulation of
one glycine in its zwitterionic form in water and obtain a PMF curve
to see if the system is equilibrated and that all possible torsions
are covered for my 100ns run. I am not sure how to approach this
issue. Is th
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