[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Tue Aug 1 23:49:59 CEST 2017

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
>> > > > --
>> > > > Gromacs Users mailing list
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