.
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Avinash Kumar.
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Dear All,
I wish to calculate the components of pressure (pressure tensor) of a group,
ie x,y and z components . Is there any any function in GROMACS which will do
it for a group as a function of height. Or do I have to write my own code
for postprocessing. Thank you.
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Avinash Kumar
mand prompt or where
?
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Avinash Kumar.
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Dear All,
I wish to calculate the components of pressure (pressure tensor) of a group,
ie x,y and z components . Is there any any function in GROMACS which will do
it for a group as a function of height. Or do I have to write my own code
for postprocessing. Thank you.
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Avinash Kumar
Hello all,
I am working on liquid vapour interfaces. How do I determine which atom is
in vapour state and which one in liquid. What thermodynamics property will
tell me that? Thank you.
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Avinash Kumar.
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Hello all,
Does anybody have a .gro and .pdb containing carbon tetrachloride? I am
having problems generating the .pdb
as the conversion to gro is not taking place correctly?
Thank you
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Hello all,
does anybody possess a sample of "pull.pdo" data file for pull codes.
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Hello all,
Is there anyway to provide constant velocity to any particular group of atoms.?
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Dear all,
Is there a way to impart a constant velocity to a group
during a simulation. That is irrespective of any interaction the
velocity will remain same during the course of the simulation.
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Dear All,
I need to define the LJ potential in a new way.
Could anybody tell me where the LJ potential is calculated in the
GROMACS files.
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Avinash Kumar.
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)
coeff1 = K (energy/distance^2)
coeff2 = R0 (distance)
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Avinash Kumar.
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Please
?
Please help me.
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4th year undergraduate,
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terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E_x = 1 0.1 0
E-xt =
E-y =
E-yt =
E-z =
E-zt =
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Avinash Kumar
nstcomm depending on a given
acceleration. Is there any criteria of deciding the above thing.
Avinash Kumar
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Hello all,
This is more of a theoretical question than relating to
the software. My question is that when we simulate a pressure driven
system (that is I am trying to simulate a nanochannel fluid flow using
GROMACS) the pressure is being implemented by defining the group of
fluid atom
where my other files
are and "s1" and "s2" are name of the groups.
Thanks in advance,
Avinash Kumar
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To Maik Goette,
Thank you for your reply.
Avinash Kumar
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ease guide me on this.
Avinash Kumar
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Hello all,
Thank you Xavier for your reply. I will explain why I want to change
the source code. I have to implement a modified Lennard Jones
potential,
⎧
⎪
⎨ 4 *epsilon{( _σ_ )^12 − (_σ_ )^6} − VLJ (rc ), r ≤ rc ,
r
Hello all,
I am trying to change the source code of GROMACS. Can
somebody assist me on this? I mean how to do this,and where actually
the changes have to be made so that software works in a modifies
manner.
Avinash
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Hello all,
I am trying to change the source code of GROMACS. Can
somebody assist me on this? I mean how to do this,and where actually
the changes have to be made so that software works in a modifies
manner.
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Hello all,
I saw a command in the analysis part of manual in section 8.14
. The command name is g_pvd . It says it can calculate properties like
density of particles per unit volume but I donot find it in the manual
nor in my GROMACS installation. Can anybody help me on this?
Avinash
outside
standard GROMACS capabilities or you only use the postprocessing commands of
GROMACS .
Avinash Kumar
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e program does nothing further . I checked for
the installation of g_rdf and found it to be installed . My simulation was
completed and for command like "trjconv" can read all the frames . Then why
is "g_rdf" command failing to read all the frames?
eagerly waiting for a reply.
,
Avinash Kumar
IIT Kharagpur
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