[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site
Ali Ahmed
aa5635737 at gmail.com
Tue Aug 1 20:05:05 CEST 2017
Hi,
Thank you for your help.
well I used this command
gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em
and I got all the warnings. Here is my em.mdp
-------------------------------------------------------------------------------------
integrator = steep
emtol = 10.0
emstep = 0.001
nsteps = 50000
energygrps = system
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1
cutoff-scheme = group
ns_type = grid
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> No, only mdrun issues LINCS warnings. grompp issues different warnings, and
> I would like you to check whether you had any from grompp that you may not
> have considered. :-)
>
> Mark
>
> On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed <aa5635737 at gmail.com> wrote:
>
> > Dear Mark
> > Yes, all the warnings are from grompp.
> > I have no idea where is the problem in the structure or the topology
> > Thank you
> >
> > On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Did you get any warnings from grompp?
> > >
> > > Mark
> > >
> > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed <aa5635737 at gmail.com> wrote:
> > >
> > > > Hello GROMACS users,
> > > >
> > > > I'm doing MD for nitrogen, and for better electrostatic interactions
> I
> > > need
> > > > to use massless and charged virtual site. I did that but when I try
> to
> > do
> > > > energy minimization gives me LINCS warning and crush. I don't know
> > where
> > > is
> > > > the error I tried a lot but could not find a solution.
> > > > Anyone has an idea where is my error
> > > >
> > > > Here is the topology file (hand written)
> > > >
> > > > ------------------
> > > >
> > > > [ defaults ]
> > > >
> > > > 1 3 yes 0.5 0.5
> > > >
> > > > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> > > ;;;;;;;;;;;;;
> > > >
> > > > [ atomtypes ]
> > > >
> > > > ; name bond_type mass charge ptype sigma
> epsilon
> > > >
> > > > OP OP 0.000 0.000 A 0.330
> 0.3062
> > ;
> > > > nitrogen
> > > >
> > > > M M 0.000 0.000 V 0.000
> > 0.000
> > > ;
> > > > virtual site
> > > >
> > > >
> > > > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> > > ;;;;;;;;;;;;;;;;
> > > >
> > > > [ moleculetype ]
> > > >
> > > > ; name nrexcl
> > > >
> > > > N2 2
> > > >
> > > >
> > > >
> > > > [ atoms ]
> > > >
> > > > ; nr type resnr residue atom cgnr charge mass
> > > >
> > > > 1 OP 1 N2 N1 1 -0.482 14.0067
> > > >
> > > > 2 M 1 N2 M1 1 0.964 0.000
> > > >
> > > > 3 OP 1 N2 N2 1 -0.482 14.0067
> > > >
> > > >
> > > >
> > > > [ constraints ]
> > > >
> > > > ; the N-N is fixed
> > > >
> > > > 1 3 1 0.11
> > > >
> > > >
> > > >
> > > > [ virtual_sites2 ]
> > > >
> > > > ; site ai aj funct a
> > > >
> > > > 2 1 3 1 0.5000 ; right in the mid
> > > >
> > > >
> > > >
> > > > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
> > > >
> > > > [ system ]
> > > >
> > > > N2 in vacuo
> > > >
> > > >
> > > >
> > > > [ molecules ]
> > > >
> > > > N2 1500
> > > >
> > > > ------------------------------------------------------------
> > > > --------------------------------------
> > > >
> > > > Here is the structure (N2.pdb)
> > > >
> > > > -----------
> > > >
> > > > TITLE N2 with dummy masses
> > > >
> > > > REMARK THIS IS A SIMULATION BOX
> > > >
> > > > MODEL 1
> > > >
> > > > COMPND UNNAMED
> > > >
> > > > AUTHOR GENERATED BY OPEN BABEL 2.3.2
> > > >
> > > > CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1
> > > >
> > > > ATOM 1 N1 N2 1 0.000 0.000 0.000 1.00
> > > > 0.00 N
> > > >
> > > > ATOM 2 M1 N2 1 0.55000 0.000 0.000 1.00
> > > > 0.00 Xx
> > > >
> > > > ATOM 3 N2 N2 1 1.100 0.000 0.000 1.00
> > > > 0.00 N
> > > >
> > > > CONECT 1 3
> > > >
> > > > CONECT 3 1
> > > >
> > > > MASTER 0 0 0 0 0 0 0 0 3 0 3
> 0
> > > >
> > > > END0
> > > >
> > > > ------------------------------------------------------------
> > > > ---------------------------------
> > > > Thank you
> > > > --
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