Thanks Mark for the explanation. Yeah, definitely I need to go through the algorithms that GROMACS use. <br>As far Table approach is concerned, same simulation set up worked without using Table.<br><br>thanks<br>sikandar<br>
<br><div class="gmail_quote">On Thu, Mar 25, 2010 at 3:43 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">On 26/03/2010 7:07 AM, Sikandar Mashayak wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
@ Xavier :: I am trying out table approach also. But I am facing some<br>
issues with it. To start with , as a test run, i use GROMACS provided<br>
table6-12.xvg table for LJ interactions. Using this table I am running<br>
water bulk simulations. In mdp file I specify to use PME for<br>
electrostatics and User for LJ by providing the table6-12.xvg file. But<br>
the simulation crashes with the notes ::t = 0.000 ps: Water molecule<br>
starting at atom 5363 can not be settled.<br>
Check for bad contacts and/or reduce the timestep.<br>
Wrote pdb files with previous and current coordinates<br>
</blockquote>
<br></div>
Did it run without using tables?<br>
<br>
Mark<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
On Thu, Mar 25, 2010 at 11:26 AM, Sikandar Mashayak<br></div><div class="im">
<<a href="mailto:symashayak@gmail.com" target="_blank">symashayak@gmail.com</a> <mailto:<a href="mailto:symashayak@gmail.com" target="_blank">symashayak@gmail.com</a>>> wrote:<br>
<br>
@ Mark :: you said if the potential is never used then I dont have<br>
to worry about storing its value. Suppose I am replacing Coulombic<br>
interactions with something of its equivalent through new force<br>
field, and I dont store the potential due to it, will I still get<br>
the similar results in terms of structure (RDF). Of course I am<br>
assuming that new force can accurately replace the Coulombic<br>
interactions among the charged atoms.<br>
<br>
By just having correct forces acting on the atoms and not worrying<br>
about storing potential energies, will I still get same trajectory<br>
as with storing potential energies.<br>
<br>
thanks<br>
sikandar<br>
<br>
<br>
On Thu, Mar 25, 2010 at 5:45 AM, XAvier Periole <<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a><br></div><div class="im">
<mailto:<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>>> wrote:<br>
<br>
<br>
If your force is between "atom" pairs you might be better trying<br>
to give all<br>
of that as a tabulated potential ... no coding.<br>
<br>
<br>
On Mar 25, 2010, at 7:14 AM, Mark Abraham wrote:<br>
<br>
<br>
<br>
----- Original Message -----<br>
From: Sikandar Mashayak <<a href="mailto:symashayak@gmail.com" target="_blank">symashayak@gmail.com</a><br></div><div class="im">
<mailto:<a href="mailto:symashayak@gmail.com" target="_blank">symashayak@gmail.com</a>>><br>
Date: Thursday, March 25, 2010 15:12<br>
Subject: Re: [gmx-users] CG Force and Potential through<br>
do_force()<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div><div class="im">
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br>
<br>
well if I need to add it by myself, I am not very sure<br>
in what variable to add it to. Like I said, I know to<br>
add the force on the atom i do f[indxofatom][XX]=<br>
forcevalue, where to potential value due to this force?<br>
<br>
<br>
It's not easy. Look at how the generic kernel does it and<br>
work you way back through the data structures.<br>
<br>
Mark<br>
<br>
On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham<br>
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br></div><div><div></div><div class="h5">
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br>
<br>
On 25/03/2010 2:42 PM, Sikandar Mashayak wrote:<br>
<br>
<br>
<br>
Hi<br>
<br>
<br>
<br>
I want to do Coarse-Grained simulation in Gromacs. I have<br>
one CG force<br>
<br>
<br>
formula, which I plan to implement by adding a short code in<br>
do_force()<br>
<br>
<br>
routine in Gromacs 4.0.7 source code.<br>
<br>
<br>
<br>
After browsing through the do_force() code, I am now<br>
familiar with data<br>
<br>
<br>
structure relevant to add the new force. I mean, I can<br>
specify new force<br>
<br>
<br>
by adding to f[indx][XX] and so on.<br>
<br>
<br>
<br>
But I am not very sure about potential, whether do I have to<br>
explicitly<br>
<br>
<br>
specify the potential on atoms due to this force or gromacs<br>
<br>
<br>
automatically takes care of it by knowing the forces on each<br>
atoms?<br>
<br>
<br>
<br>
<br>
You will need to add that yourself if you want the reported<br>
potential to be accurate. GROMACS uses the given parameters<br>
in its inner loops to calculate energies and forces. The<br>
former are not reverse-engineered from the latter. If the<br>
potential is never used, however, then you can forget about<br>
it...<br>
<br>
<br>
<br>
<br>
Mark<br>
<br>
<br>
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