[gmx-users] Error with tabulated potential and tip4p water model

[Udaya Dahal]

Thank you mark for the reply. But here i have only one polymer which i used
optimized structure polymer and used genbox to generate box of solvent
which obviously puts the water at different lattice points. It was never a
problem to simulate when I was using the LJ potential. So, my concern here
is about how the gromacs reads the table internally.

So far, in the table, what I did is; I made all f,f',h,h' columns zero and
calculated the total (sum of electrostatics+LJ/Buckingham+user defined
potential) potential and put in the column g and the negative derivative of
g in g' column thereby putting all the coefficients as 1 in the .itp file.
When I try to use that table it gives me the warning that the
derivative(-force) deviates from the potential by 164%(one example). While
reading the Manual, I found that it uses the Cubic splines Algorithm to
regenerate the table internally. I am not sure if that algorithm was not
compatible with the way i created the table(for potential) or it is
something else. Looks like I am lost somewhere in between here because EM
was never a great problem until I used the tabulated potential.


Udaya


On Tue, Aug 5, 2014 at 10:38 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Generating a sane starting structure is not really in GROMACS problem
> space. You should take steps to ensure atoms are not closer to each other
> than is physically reasonable, and probably start with the coordinates of
> each molecule whole with respect to PBC. Start with a single polymer
> solvated, then perhaps use genconf to add complexity.
>
> Mark
>
>
> On Mon, Aug 4, 2014 at 8:48 AM, Udaya Dahal <dahal.udaya at gmail.com> wrote:
>
> > It was immediate. But I figured out the way to solve that issue. Looks
> > like  the starting initial configuration was not so good. A different
> > starting structure at least gave me the energy minimization to few steps
> > but I kind of really find very hard to have the energy minimized to
> smaller
> > value.  The maximum force on the particular atom is around ...+03. Do I
> > really have to amend each and every atom step by step(which still doesn't
> > solve the problem) or there is any other specific way that we can get
> > more/less energy minimized structure. Thank you for your help.
> >
> >
> > On Sun, Aug 3, 2014 at 9:23 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Immediately, or after some EM steps?
> > >
> > > Mark
> > >
> > >
> > > On Sun, Aug 3, 2014 at 12:56 PM, Udaya Dahal <dahal.udaya at gmail.com>
> > > wrote:
> > >
> > > >  I have tabulated potential for all the possible combinations(non
> > > bonded).
> > > > I am using Tip4p water model for the polymer water interaction. While
> > > > running the energy minimization i got the error like below.
> > > >
> > > > Fatal error:
> > > > Settle block crossing node boundaries
> > > > constraint between atoms 664, 665, 666)
> > > > For more information and tips for troubleshooting, please check the
> > > GROMACS
> > > > website at http://www.gromacs.org/Documentation/Errors
> > > >
> > > > Any idea to slove this issue.?
> > > >
> > > > Thank you,
> > > > Udaya.
> > > > --
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> > --
> > Udaya Dahal,
> > Graduate Assistant,
> > Department of Physics,
> > University of Connecticut
> > --
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