[gmx-users] regarding table for water water interactions

sreelakshmi ramesh sree.lakshmi at research.iiit.ac.in
Wed May 25 12:50:31 CEST 2011

Dear Mark,
                  Thanks for your reply.It cleared my doubts.I have one more
doubt.i first tried to just minimize the system ( the same spc model).using
amber03 and lennard jones6-12 potential.system was well minimized and got

Now i tried copying the same  table6-12.xvg,  file from gromax lib to my
current directory.
1.changed the  first adn second parameter to 1 in defaults section in
amber03 ff.itp
2.since ffnonbonded section is in terms of sigma and epsilon i converted the
sigma and epilon columns to A and B (a=4epsi^6 adn b=4epsi8sig^12)
3.now i just included the folling line in em.mdp file


renamed table_6_12.xvg to table.xvg
then i grompped it
* grompp -f em.mdp -c saltwater.gro -p topol.top -o em.tpr  -maxwarn 3*
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
Generated 2278 of the 2278 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2278 of the 2278 1-4 parameter combinations
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'
Analysing residue names:
There are:  2961      Water residues
Number of degrees of freedom in T-Coupling group rest is 26646.00
Largest charge group radii for Van der Waals: 0.039, 0.039 nm
Largest charge group radii for Coulomb:       0.084, 0.084 nm
This run will generate roughly 5 Mb of data

Back Off! I just backed up em.tpr to ./#em.tpr.2#

gcq#42: "Out Of Register Space (Ugh)" (Vi)

then mdrun
  * mdrun -s em.tpr  -o em.trr -e em.edr *
Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =         2000

Reached the maximum number of steps before reaching Fmax < 1000

writing lowest energy coordinates.

Back Off! I just backed up confout.gro to ./#confout.gro.2#

Steepest Descents did not converge to Fmax < 1000 in 2001 steps.
Potential Energy  =  1.5031059e+07
Maximum force     =  3.4432207e+04 on atom 1357
Norm of force     =  6.4161267e+02

gcq#197: "I Do It All the Time" (Magnapop)

Now my  questions are

1. I had experimented with the same potential 6-12 but why didnt the sys
didnt get converged when i usethe same orginal potential  as user  specified
2.are there any other terms to be included  apart Fromm table in .mdp file ?

added theses lines in topolgy

On Wed, May 25, 2011 at 3:21 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> On 25/05/11, *sreelakshmi ramesh * <sree.lakshmi at research.iiit.ac.in>
> wrote:
> Hai all,
>           My system is just a water Spc model.
>           I am trying to create a table.xvg which would deal with nonbonded
> intearction for water-water for say SPC model.
> If i have to calculate the potential i have to consider the  interaction
> between
> 1.O of water1--O of water 2(LJ+COLOUMB)  [CREATED A TABLE that containsr, f
> (r), -f (r), g(r),-g (r), h(r) and -h (r) ]
> 2.H of water 1--O of water 2(COLOUMB)        [ are tables needed ?]
> 3.H of water 1--H of water 2(COLOUMB)         [are tables needed ?]
> That depends whether you're trying to apply a different or the same
> functional form to the interactions of the hydrogen atoms, i.e. whether you
> have an energy group for the whole system, or have O and H in different
> energy groups so that you can apply different functional forms to different
> interactions.
> for 2 and 3rd case should i create 2 tables respectively ? if not how is
> the potential is calculated  for the the last two cases ?
> The user table applies to all interactions unless you start playing around
> with energygrp_table. So your hydrogen interactions use the table, but only
> look up the values for f.
> and if it has to be to created since the lennard jones part say g(r),-g
> (r), h(r) and -h (r) is zero for all values of r should i just create a
> table with r,f(r)and -f'(r) for last two cases?
> 6.7.2 covers this last point.
> Mark
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