On 26/03/2010 7:56 AM, Sikandar Mashayak wrote:
Thanks Mark for the explanation. Yeah, definitely I need to go through
the algorithms that GROMACS use.
As far Table approach is concerned, same simulation set up worked
without using Table.
Well, you've probably done it wrong, but we don't have enough
information to say where...
Mark
On Thu, Mar 25, 2010 at 3:43 PM, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
On 26/03/2010 7:07 AM, Sikandar Mashayak wrote:
@ Xavier :: I am trying out table approach also. But I am facing
some
issues with it. To start with , as a test run, i use GROMACS
provided
table6-12.xvg table for LJ interactions. Using this table I am
running
water bulk simulations. In mdp file I specify to use PME for
electrostatics and User for LJ by providing the table6-12.xvg
file. But
the simulation crashes with the notes ::t = 0.000 ps: Water molecule
starting at atom 5363 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Did it run without using tables?
Mark
On Thu, Mar 25, 2010 at 11:26 AM, Sikandar Mashayak
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
@ Mark :: you said if the potential is never used then I
dont have
to worry about storing its value. Suppose I am replacing
Coulombic
interactions with something of its equivalent through new force
field, and I dont store the potential due to it, will I
still get
the similar results in terms of structure (RDF). Of course I am
assuming that new force can accurately replace the Coulombic
interactions among the charged atoms.
By just having correct forces acting on the atoms and not
worrying
about storing potential energies, will I still get same
trajectory
as with storing potential energies.
thanks
sikandar
On Thu, Mar 25, 2010 at 5:45 AM, XAvier Periole
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
If your force is between "atom" pairs you might be
better trying
to give all
of that as a tabulated potential ... no coding.
On Mar 25, 2010, at 7:14 AM, Mark Abraham wrote:
----- Original Message -----
From: Sikandar Mashayak <[email protected]
<mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>
Date: Thursday, March 25, 2010 15:12
Subject: Re: [gmx-users] CG Force and Potential through
do_force()
To: Discussion list for GROMACS users
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>
well if I need to add it by myself, I am not
very sure
in what variable to add it to. Like I said, I
know to
add the force on the atom i do f[indxofatom][XX]=
forcevalue, where to potential value due to this
force?
It's not easy. Look at how the generic kernel does
it and
work you way back through the data structures.
Mark
On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham
<[email protected] <mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>> wrote:
On 25/03/2010 2:42 PM, Sikandar Mashayak wrote:
Hi
I want to do Coarse-Grained simulation in Gromacs. I
have
one CG force
formula, which I plan to implement by adding a short
code in
do_force()
routine in Gromacs 4.0.7 source code.
After browsing through the do_force() code, I am now
familiar with data
structure relevant to add the new force. I mean, I can
specify new force
by adding to f[indx][XX] and so on.
But I am not very sure about potential, whether do I
have to
explicitly
specify the potential on atoms due to this force or
gromacs
automatically takes care of it by knowing the forces
on each
atoms?
You will need to add that yourself if you want the
reported
potential to be accurate. GROMACS uses the given
parameters
in its inner loops to calculate energies and forces. The
former are not reverse-engineered from the latter.
If the
potential is never used, however, then you can
forget about
it...
Mark
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