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

[Mark Abraham]

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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