[gmx-users] Increase the box size or decrease rlist

[Mark Abraham]

You can't have a sensible bilayer with atomistic water and have no charged
atoms! Please reconsider however you are generating that input.

Mark


On Wed, Aug 20, 2014 at 4:33 PM, pragna lakshmi <pragnapcu at gmail.com> wrote:

> I could solve the fatal error by giving box vectors 4.84331 4.84331 6.69130
> while generating .gro file from .pdb using editconf.
> Then, the following warning:
> WARNING 1 [file minim.mdp]:
>   You are using full electrostatics treatment PME for a system without
>   charges.
>   This costs a lot of performance for just processing zeros, consider using
>   Cut-off instead.
>
>
> So, should i give -maxwarn 1 or change the electrostatics from 'PME' to
> 'Cut-off'. Can anyone please suggest?
>
> Thanking You,
>
>
>
> On Wed, Aug 20, 2014 at 8:55 AM, pragna lakshmi <pragnapcu at gmail.com>
> wrote:
>
> > Thank u Justin for your reply.
> > I have realized that stockholm lipids are derived from Amber ff. But i am
> > unable to get parameters for POPC derived from charmm ff. Is there any
> > source for that?
> > The box vectors that are listed in POPC.gro are    0.00000   0.00000
> > 0.00000
> >
> >
> >
> > On Tue, Aug 19, 2014 at 11:50 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 8/19/14, 2:14 PM, pragna lakshmi wrote:
> >>
> >>> Dear all,
> >>> I am trying to do MD simulation of POPC membrane simulation with
> >>> peripheral
> >>> attachment of protein ligand complex. Steps that i have performed so
> far
> >>> are:
> >>>
> >>> 1. orienting the protein with editcong -princ command
> >>> 2. rotating it along the y-axis with editconf -rotate 0 40 0 command
> >>> 3. separation of protein ligand files into individual files and
> >>> generation
> >>> of topology file of protein from pdb2gmx and ligand from swissparam.
> >>> (charmm 36ff was used for protein topology generation. source:
> >>> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs )
> >>> 4. The protein and ligand files were merged followed by necessary
> changes
> >>> in topology file.
> >>> 5. Pre-equilibrated POPC bilayer was downloaded from Dr.Klauda's
> website
> >>> whereas its itp file was taken from Stockholm_Lipids website.
> >>>
> >>
> >> The Stockholm lipids are derived from Amber force fields.  You can't
> >> combine them with CHARMM protein parameters and expect anything
> physically
> >> meaningful. If you're using the CHARMM protein force field, use the
> CHARMM
> >> lipid parameters.
> >>
> >>
> >>  6. After this, when i am running the command
> >>> grompp -f minim.mdp -c POPC.gro -p POPC.top -o em_POPC.tpr
> >>> i am facing the fatal error:
> >>> ERROR: The cut-off length is longer than half the shortest box vector
> or
> >>>    longer than the smallest box diagonal element. Increase the box size
> >>> or
> >>>    decrease rlist.
> >>>
> >>
> >> What are the box vectors listed in POPC.gro?
> >>
> >>
> >>  As it is suggesting, I have decreased rlist, rcoulomb and rvdw from 1.2
> >>> to
> >>> 1.0. But still the same error is raising.
> >>>
> >>
> >> Don't mess with these settings just to make an error message go away.
> >> The nonbonded setup is a fixed feature of the force field, and lipids
> are
> >> especially sensitive to changes here.  I just posted the proper settings
> >> for the CHARMM force field a few days ago; use those settings and don't
> >> deviate unless you have proof that what you're doing is superior.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 601
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
> >> --
> >> Gromacs Users mailing list
> >>
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> >>
> >
> >
> >
> > --
> > Pragna Lakshmi.T,
> > Ph.D. Scholar,
> > IPLS Project,
> > Pondicherry University,
> > Pondicherry,
> > India - 605014.
> >
>
>
>
> --
> Pragna Lakshmi.T,
> Ph.D. Scholar,
> IPLS Project,
> Pondicherry University,
> Pondicherry,
> India - 605014.
> --
> Gromacs Users mailing list
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