, battis...@libero.it wrote:
Dear Carsten
could you give me more information about your suggestions?
I tried but probably I did not understand well what you meant.
Hi Anna,
I suggested to use the enforced rotation module of Gromacs 4.6
to restrain the orientation of your molecule(s). If you want
). For more info you may want to
look at this page:
http://www.mpibpc.mpg.de/grubmueller/rotation
Best,
Carsten
On Jul 23, 2013, at 12:18 PM, battis...@libero.it wrote:
Dear user and expert,
I'd like ask you a suggestion about a problem that I will try present you
schematically.
I have got
...@libero.itbattis...@libero.it, Discussion list for GROMACS
usersgmx-users@gromacs.org
Ogg: Re: [gmx-users] Rotation Constraints - PMF + rerun
On Jul 24, 2013, at 12:30 PM, battis...@libero.it wrote:
Dear Carsten,
Thank you very much for your very useful help!
I'm making some tries to test
to zero. There is also a 4.5 add-on available with rotational restraints in
the Gromacs git repository (branch rotation). For more info you may want to
look at this page:
http://www.mpibpc.mpg.de/grubmueller/rotation
Best,
Carsten
On Jul 23, 2013, at 12:18 PM, battis...@libero.it wrote:
Dear user
Dear user and expert,
I'd like ask you a suggestion about a problem that I will try present you
schematically.
I have got a structure s and I have generated the topolgy file itp for it.A
number of separate s in turn generate a complex structure A, that is
characterized by a cylindrical shape.
Dear users and experts
I'm doing an umbrella-samplig calculation to obtain the PMF when two structure
(A and B) are at various X distances.
I setted my md-umbrella.mdp file as in follows:
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = umbrella
Dear users and experts
I'm doing an umbrella-samplig calculation to obtain the PMF when two structure
(A and B) are at various X distances.
I setted my md-umbrella.mdp file as in follows:
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull =
/13 11:03 AM, battis...@libero.it wrote:
Dear users and experts,
why the angle calculated by g_sgangle, that are given in degrees, are only
in the range (-1, 1)?
The format of g_sgangle is time, cos(angle), angle. Since values of cos
(angle)
are within { -1, 1 } that explains what you
Dear users and experts,
do you know if it is possible make the bending angle calculation in the
following case?
I have got three groups (G1, G2, G3) into a system.
I have to define the center of mass of each one. I have to calculate the
bending angle defined by vector 1 and vector 2.
vector
Dear users and experts,
why the angle calculated by g_sgangle, that are given in degrees, are only in
the range (-1, 1)?
Many thanks,
Anna
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Dear all,
I'm trying install do_dssp on my pc.I followed the steps indicated in the page:
http://lists.gromacs.org/pipermail/gmx-users/2010-November/055728.html
1.step-root at ab-desktop:/path-dsspcmbi.tar.gz/# tar xvzf dsspcmbi.tar.gz
2.step-root at
Dear all,
is it possible to put into a box a defined number of particle?in other word,
i'd like put into my system eg. 100 molecule of water, I tried with:
genbox -cp protein.gro -cs -nmol 100 -try 1 -o out.gro
but it does not work.Can you help me?
Thanks!
Anna
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I solved with
genbox -cp conf.gro -cs -maxsol 100 -p topol.top -o out.gro
Thanks!
Anna--
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Dear all,
I got some question about the implicit solvent.1) In gromacs, is it possible
simulate a protein in a layer of explicit water, and put this system (protein
+ SOL) into a big box and make the MD simulation with implicit solvent? How I
have to set the md.mdp parameter (; IMPLICIT
Dear Mark,
about point 2, yes I need to have
a uniform distribution of a defined numberof water molecule (eg. 100 water
molecule ) into my box.
Is it possible with genbox?
After, I'll have to make the md simulation for my
system in implicit solvent
(I'll have protein + 100 molecule SOL +
Thank you very much for your suggestions!
Anna
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Dear all,
thanks a lot for your suggestions that give me the possibility to improve my
calculation.
All the best
Anna
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Dear all
I'd like to get the PMF using g_wham after umbrella sampling. I saw that PMF
profile dipend very strong from the windows selected in the z (reaction
coordinate) direction.
My idea is that the result of this method is much more qualitative than
quantitative. Are you in agreement with
Dear all,
I have got a question about the PMF profile determined with umbrella sampling
calculation.
If z is the reaction coordinate, is it possible to calculate a PMF profile
with umbrella sampling if we have a repulsive force at 0za, a minimum of
energy at z=a and an actrattive force for
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