[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site
Ali Ahmed
aa5635737 at gmail.com
Wed Aug 2 00:07:22 CEST 2017
Dear Dr. Dallas,
Thank you for your reply. Actually, I'm new to GROMACS and
I appreciate your support.
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Here is what I get before crashing. Too many warning then crush.
Step 37, time 0.037 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.002768, max 0.195102 (between atoms 34930 and 34931)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
193 194 51.7 0.1100 0.1100 0.1100
54409 54410 32.3 0.1100 0.1100 0.1100
On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren <dallas.warren at monash.edu>
wrote:
> Copy the output from both of those commands, most importantly (as Mark
> has asked) that from the first one gmx grompp
>
> You need to show people exactly what you are seeing, not what you say
> you are seeing. The latter you are filtering it, and most likely not
> providing all the important information. The former allows those
> trying to help to see all the information that they need to see.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 2 August 2017 at 04:05, Ali Ahmed <aa5635737 at gmail.com> wrote:
> > 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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