[gmx-users] Problem with tabulated potentials for 3 different atoms

[Gareth Tribello]

Dear Martin

As Mark has already told you - if you have a problem with gromacs  email the
list and wait for a reply.  Don't just email people you don't know from Adam
and expect them to reply because "you are in a rush."  The file that you
have read from the mailing list contains everything I know about tabulated
potentials in gromacs. I can't say I fully understand your email but I think
that your questions (other than the stuff on bonded potentials) are all
covered on the wikki page and certainly are covered in the pdf file I wrote.


In short

>For the bonding part I have the following table files:

>table_b1.xvg
>table_a1.xvg
>table_a2.xvg
>table_a3.xvg

I know nothing about using tabulated potentials for bonded interactions.  If
this is what is in the manual though its probably right.


> Must I write
>
> energygrps      = A B C
> energygrp_table = AC BB BC
>
> in the mdp file and use the tables
>
> table.xvg                        This has the A B interaction in?
> table_A_C.xvg
> table_B_B.xvg
> table_B_C.xvg
>
> with the command line for mdrun saying -table table.xvg?
>

Yes this is exactly what the wikki tells you to do. Why do you think it wont
work in your case?  Incidentally,  you can work out if this is working by
doing one md step in gromacs and comparing the energy you obtain with the
energy you get from another code, which you are confident produces correct
energies.

Another thing, because the tables doesn't have to contain only zero
> columns...
> Can I put anything on the f and f' columns (because the charge of my
> atoms is zero)?
>

Yes.  I always use f=1/r even though I know it will be ignored (with this
choice f'=1/r**2 obviously)


> Can I put (for example) 0.5 in the g and g' columns and my potential
> (and the force) minus 0.5 in columns h and h'?
>

I don't understand what you want to do here.  If you put 0.5 in g then g'=0,
which you can work out using, what I assume, is the first thing you learnt
about calculus.

ciao
Gareth
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100419/97fdb99d/attachment.html>