[gmx-users] Problem implementing REST

[Mark Abraham]

Hi,

Thanks for the links. Offhand, I don't know the answers to your questions
and don't have time to look into it now. You should certainly ask them how
they did it. One work-around might be to do the necessary trig to convert
sums-of-Fourier dihedrals to a Ryckaert-Bellemans dihedral, and the issue
of type 9 and lambda interpolation goes away.

Mark

On Thu, Oct 16, 2014 at 3:03 PM, carlo martinotti <specialkender at hotmail.com
> wrote:

> I'm running GROMACS version 4.6.3, it seems that the hyperlinks doesn't
> work in the mailing list, so i'll post the links to my files (perturbed
> atoms are indicated by the "&"):
> mdp > http://textuploader.com/oj7qtop >
> http://textuploader.com/oj7cffbonded >
> http://textuploader.com/oj7mffnonbonded >  http://textuploader.com/oj7h
> The issue seems to be regargind lines in topology which correspond to
> proper dihedrals (function 9). Actually i've gone in the ffbonded file and
> i tried to delete the perturbed proper dihedrals, but then again it would
> give one error and one warning for each of the dihedrals as this one :
>
> ERROR 48 [file topol2.top, line 222]:  Cannot automatically perturb a
> torsion with multiple terms to different  form.  Please specify perturbed
> parameters manually for this torsion in your  topology!
>
> WARNING 48 [file topol2.top, line 222]:  No default Proper Dih. types for
> perturbed atoms, using normal values
>
> The problem seems to be as it follows:
> The author in the article claims to have made everything with the lambda
> system , but lambda system seems not able to perturb dihedrals with
> multiple terms, nor to use the same terms in state A and B. So, can i solve
> the problem and still use lambda system to interpolate betwen the 2
> hamiltonians?
> In case i can't, can i build one complete topology file for each replica
> that i want to simulate, perturb the topology modifying the hamiltonian
> consequently and then run a replica exchange  with the REMD routine?
> Wouldn't it be the same thing as using the lambda system, except it would
> be better because you can use verlet cutoff scheme, and so, also, GPUs?
>
>
> > Date: Thu, 16 Oct 2014 12:04:38 +0200
> > From: mark.j.abraham at gmail.com
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Problem implementing REST
> >
> > Hi,
> >
> > What GROMACS version is this? What bits of your topology are being
> > complained about?
> >
> > Mark
> >
> > On Thu, Oct 16, 2014 at 11:12 AM, carlo martinotti <
> > specialkender at hotmail.com> wrote:
> >
> > > I'm currently trying to implement Replica Exchange with Solute
> Tempering
> > > in gromacs, as previously done by terakawa et al (On easy
> implementation of
> > > a variant of the replica exchange with solute tempering in GROMACS, J
> > > Comput Chem. 2011 May;32(7):1228-34. doi: 10.1002/jcc.21703. Epub 2010
> Nov
> > > 29.)
> > > From what i understood you have to change ffnonbonded.itp adding new
> > > atomtypes with perturbed LJ parameters, then change ffbonded.itp
> adding new
> > > bond/angles and dihedral types between this perturbed atoms with
> modifed
> > > harmonic constant, and that's it for the forcefield.
> > > Then you have to prepare a topology with state A and state B with
> state B
> > > having perturbed charges and the atom types corresponding to the
> perturbed
> > > version of the state A atoms.
> > > Now, i have some problems. I'm trying to modify amber03 forcefield, but
> > > when i try to run grompp it gives me this errors:
> > >
> > > ERROR 1 [file topol.top, line 199]:  Cannot automatically perturb a
> > > torsion with multiple terms to different  form.  Please specify
> perturbed
> > > parameters manually for this torsion in your  topology!
> > > ERROR 2 [file topol.top, line 202]:  Cannot automatically perturb a
> > > torsion with multiple terms to different  form.  Please specify
> perturbed
> > > parameters manually for this torsion in your  topology!
> > >
> > > ERROR 3 [file topol.top, line 205]:  Cannot automatically perturb a
> > > torsion with multiple terms to different  form.  Please specify
> perturbed
> > > parameters manually for this torsion in your  topology!
> > >
> > > ERROR 4 [file topol.top, line 206]:  Cannot automatically perturb a
> > > torsion with multiple terms to different  form.  Please specify
> perturbed
> > > parameters manually for this torsion in your  topology!
> > > Now, it seems that gromacs can't do this operation with amber, but in
> the
> > > article that i read they actually used amber03, so what should i do?
> This
> > > are my files mdp top ffbonded ffnonbonded
> > > Can somebody explain me where is the problem?
> > > --
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