[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site
Justin Lemkul
jalemkul at vt.edu
Wed Aug 2 19:04:50 CEST 2017
On 8/2/17 9:12 AM, Ali Ahmed wrote:
> Dear all,
> Thank you for helping me. All I get from grompp is this
> ----------------------------------------------------------------------
>
> gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o
> topol.tpr
>
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'cpp'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
>
> NOTE 1 [file grompp.mdp]:
> The group cutoff scheme is deprecated since GROMACS 5.0 and will be
> removed in a future release when all interaction forms are supported for
> the verlet scheme. The verlet scheme already scales better, and it is
> compatible with GPUs and other accelerators.
>
> Setting the LD random seed to 1000542586
> Generated 120 of the 120 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 120 of the 120 1-4 parameter combinations
> Excluding 2 bonded neighbours molecule type 'N_2'
> Cleaning up constraints and constant bonded interactions with virtual sites
> Analysing residue names:
> There are: 2493 Other residues
Simplify your system - work with one molecule and print out the forces at each
step to see if there is something haywire going on.
-Justin
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Number of degrees of freedom in T-Coupling group System is 12462.00
>
> NOTE 2 [file grompp.mdp]:
> You are using a plain Coulomb cut-off, which might produce artifacts.
> You might want to consider using PME electrostatics.
>
>
> Largest charge group radii for Van der Waals: 0.056, 0.056 nm
> Largest charge group radii for Coulomb: 0.056, 0.056 nm
> This run will generate roughly 90 Mb of data
>
> There were 2 notes
>
> Back Off! I just backed up topol.tpr to ./#topol.tpr.1#
>
> gcq#454: "I never see what has been done; I only see what remains to be
> done." (Marie Curie)
>
>
> On Tue, Aug 1, 2017 at 5:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 8/1/17 6:07 PM, Ali Ahmed wrote:
>>
>>> 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.
>>>
>>>
>> This is not diagnostic of anything useful. You've been asked several
>> times to provide the output of grompp, not mdrun. The grompp output can be
>> suggestive of issues you may not have considered.
>>
>> -Justin
>>
>>
>> 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
>>>>>>>>> --
>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>
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>>>>
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>>>>>>
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> 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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--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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