[gmx-users] LJ potential

Wed Sep 1 22:04:27 CEST 2010

Questions inline...

On Mon, Aug 30, 2010 at 7:25 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> ----- Original Message -----
> From: Sai Pooja <saipooja at gmail.com>
> Date: Tuesday, August 31, 2010 2:45
> Subject: Re: [gmx-users] LJ potential
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
>  >
> > Thanks Mark. I have just 2 more queries regarding this.
> >
> *> When using tables for the potential, *
> >
> > 1) For VdW interactions, it it alright to use the topology
> file generated by pdb2gmx using a forcefield (eg. CHARMM27) which specifies
> LJ paramters as 'sigma' and 'epsilon' instead of C6 and C12 as in the case
> of user defined potentials?
> >
> > I ask this because I get a warning when I try to do the above:
>  > :WARNING 2 [file initffd.top, line 8082]:
> >   Using sigma/epsilon based combination rules with user supplied
> potential
> >   function may produce unwanted results
>
> You will need to take suitable care. grompp will only use the combination
> rules if it cannot find an existing definition for that pair of atomtypes,
> so if you make all the definitions, you should be OK. A good way to test
> that you are on the right track is whether you can produce an energy group +
> table file that will reproduce the result GROMACS gets if you leave it
> alone.
>

Mark I apologize but I did not understand your reply.. let me rephrase the
question(I hope to get it right this time):

In the table syntax... LJ potential uses the functional form with C6 and C12
rather tha sigma and epsilon.

The forcefield files however specify sigma and epsilon for atom pairs.

Now, if I want to use the *sigma and epsilon values in the forcefield file
along with tables for energy calculation *do I need to change the forcefield
files sigma and epsilon parameters to C6 and C12? If not, is there something
else I must do for this to work?

>
>  > 2) If one is interested in using PME for electrostatic interactions but
> with different electrostatic interaction functions for different pairs of
> energygrps, is it alright to specify the simple coulomb function in the user
> defined table and use the PME-User option for coulombtype?
>
>
Probably not. The form of the reciprocal-space PME term presupposes a simple
Coulomb function on all atoms. So did the parameterization of the force
field, so you're already taking your life in your hands :-)

How about a simple coulomb function multiplied by a constant?

Pooja

  > On Sun, Aug 29, 2010 at 7:54 PM, Mark Abraham
<mark.abraham at anu.edu.au>wrote:
>
>> >
>> >
>> > ----- Original Message -----
>> > From: Sai Pooja <saipooja at gmail.com>
>> > Date: Monday, August 30, 2010 3:33
>> > Subject: Re: [gmx-users] LJ potential
>> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> >
>> > > Hi,
>> > >
>> >
>>  > > I am simulating a system of a protein in water. I am trying to run
>> the simulation with a modified protein-water LJ and coulomb interaction.
>> Since LJ and  coulomb interaction parameters are defined at the atomic level
>> in the forcefield files, I cannot figure out a good way to modify them for
>> protein-water interactions specifically. In other words, I want to modify
>> the protein water interaction without altering protein-protein interaction.
>> >
>> > Right, that's totally different from your first question, which implied
>> only protein and thus intra-molecular interactions. When seeking help, you
>> should make sure you  make a complete description the first time, lest you
>> waste everybody's time and effort. That's easier said than done, but you
>> managed to do it on the second attempt :-)
>> >
>> > GROMACS allows you to use table lookups for non-bonded interactions,
>> and to use different tables for interactions between different energy
>> groups. So your problem reduces to generating the different tables and
>> groups, and assigning tables to pairs of groups. Aspects of this process are
>> discussed in several places in the manual.
>> >
>> > Mark
>>  >
>> >
>> > > On Tue, Aug 24, 2010 at 8:31 AM, Florian Dommert <
>> dommert at icp.uni-stuttgart.de> wrote:
>>
>>> > > -----BEGIN PGP SIGNED MESSAGE-----
>>> > > Hash: SHA1
>>> > >
>>> > > On 08/24/2010 02:27 PM, Sai Pooja wrote:
>>> > > > Hi,
>>> > > >
>>> > > > If there are n types of atoms in protein, how does one specify:
>>> > > > 1) Different types of LJ non-bonded interactions for different
>>> pairs?
>>> > > > 2) Modified Coloumb(by a pre-multiplier) interactions for
>>> different pairs?
>>> > > >
>>> > > > Pooja
>>> > > >
>>> > > >
>>> > >
>>> > > Hi,
>>> > >
>>> > >  this can be defined in the top file. Take a look at the manual
>>> > > regarding the force field and different function types for the
>>> nonbonded
>>> > > interactions. This will surely help.
>>> > >
>>> > > /Flo
>>> > >
>>> > > - --
>>> > > Florian Dommert
>>> > > Dipl.-Phys.
>>> > >
>>> > > Institute for Computational Physics
>>> > >
>>> > > University Stuttgart
>>> > >
>>> > > Pfaffenwaldring 27
>>> > > 70569 Stuttgart
>>> > >
>>> > > Phone: +49(0)711/685-6-3613
>>> > > Fax:   +49-(0)711/685-6-3658
>>> > >
>>> > > EMail: dommert at icp.uni-stuttgart.de
>>> > > Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>>> > > -----BEGIN PGP SIGNATURE-----
>>> > > Version: GnuPG v1.4.10 (GNU/Linux)
>>> > > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>>> > >
>>> > > iEYEARECAAYFAkxzu7wACgkQLpNNBb9GiPlGAQCghZWQobj9j2SqvYC1gU5e3QR9
>>> > > WVQAnAjv9tZ6xGRhc+S1vSSQh9kek4xZ
>>> > > =T+Yb
>>> > > -----END PGP SIGNATURE-----
>>>  > > --
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>>  > >
>> > >
>> > >
>> > > --
>> > > Quaerendo Invenietis-Seek and you shall discover.
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> >
> >
> >
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-- 
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