Re: [gmx-users] Lincs warning and Bond length not finite

[Mohamed Abdelaal]

Many thanks Alex for your reply :)

You have pressure scaling and LINCS convergence issues, suggesting that
> the starting configuration is far from equilibrium, as well as
> potentially other issues.
>
> How to check if my starting configuration is far from equilibrium ? I
checked the Temperature and Pressure curves ( attached in the original
email) and they look equilibirated. Is there anything I am missing?


> Gromos FF is not appropriate for graphene, and neither is turning C-C
> bonds into LINCS constraints, as set by your 'all-bonds' -- graphene is
> not a small organic molecule or a protein. Also, if your system is
> periodic in all directions, make sure the graphene edges are
> crystallographically commensurate with respect to PBC and the box size
> is appropriate.


How can I make that my graphene edges are crystallographically commensurate
with respect to PBC ?

I have chosen box size equal to the graphene sheet size and increased the
height to make sure that the deposited molecules will not be deposited out
of my graphene sheet area.


> Finally, make sure that the small molecules you're
> depositing on graphene are properly pre-equilibrated.
>
> Actually, after your email, I did the simulation for both the graphene
sheet and the deposited molecules (C60) each alone to check with one has
problems with the lincs warning. The C60 alone was successfully completed.
The Graphene sheet didn't work due to the lincs warning. I know now that
the problem is only in the graphene sheet.


> Alex
>
>
Thanks,
Mohamed



> On 5/3/2020 6:39 PM, Mohamed Abdelaal wrote:
> > Hello everyone,
> >
> > I am simulating  the evaporation of non protein molecules on a graphene
> > sheet. I am using gromos force field and hence the lincs constrain are
> set
> > to all-bonds.  I have done the energy minimization and NVT
> > successfully without any warnings. During the NPT equilibiration I got
> > Lincs warning but the NPT equilibiration was completed to the end. During
> > the md production run, I received lincs warning and Bond length not
> finite
> > and sometimes I received " nonbonded interaction between particles is
> > larger than the table limit 2.437 nm".
> >
> > I have read that this means that my system is blowing up. Hence, I have
> > read the Blowing up and diagnosing unstable system  on gromacs website, I
> > can't recognize  any of the posted issues in my files/simulation and
> > hence,  I can't decide what exactly is the problem or what should I
> change
> > (it seems that my system is well minimized and the temperature and
> pressure
> > looks fine). I have added in the below link, the NPT and md logs  and
> .mdp
> > files and pictures for the potential energy, Temperature, Pressure and
> > Density.
> >
> > https://drive.google.com/drive/folders/1yyUJNg4yXnPfsxZ9gQ4LV5sqRKnJq9rF
> >
> > I have tried the simulation again with none as  lincs constrains and it
> > worked without any errors.
> >
> > I think the problem has something to do with the pressure since the
> problem
> > started during the NPT, but I don't know how exactly to find the problem.
> > Can anyone guide me please what should I change or how should I start ?
> >
> > Thanks,
> > Mohamed
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Re: [gmx-users] Lincs warning and Bond length not finite

[Alex]

You have pressure scaling and LINCS convergence issues, suggesting that 
the starting configuration is far from equilibrium, as well as 
potentially other issues.


Gromos FF is not appropriate for graphene, and neither is turning C-C 
bonds into LINCS constraints, as set by your 'all-bonds' -- graphene is 
not a small organic molecule or a protein. Also, if your system is 
periodic in all directions, make sure the graphene edges are 
crystallographically commensurate with respect to PBC and the box size 
is appropriate. Finally, make sure that the small molecules you're 
depositing on graphene are properly pre-equilibrated.


Alex

On 5/3/2020 6:39 PM, Mohamed Abdelaal wrote:

Hello everyone,

I am simulating  the evaporation of non protein molecules on a graphene
sheet. I am using gromos force field and hence the lincs constrain are set
to all-bonds.  I have done the energy minimization and NVT
successfully without any warnings. During the NPT equilibiration I got
Lincs warning but the NPT equilibiration was completed to the end. During
the md production run, I received lincs warning and Bond length not finite
and sometimes I received " nonbonded interaction between particles is
larger than the table limit 2.437 nm".

I have read that this means that my system is blowing up. Hence, I have
read the Blowing up and diagnosing unstable system  on gromacs website, I
can't recognize  any of the posted issues in my files/simulation and
hence,  I can't decide what exactly is the problem or what should I change
(it seems that my system is well minimized and the temperature and pressure
looks fine). I have added in the below link, the NPT and md logs  and .mdp
files and pictures for the potential energy, Temperature, Pressure and
Density.

https://drive.google.com/drive/folders/1yyUJNg4yXnPfsxZ9gQ4LV5sqRKnJq9rF

I have tried the simulation again with none as  lincs constrains and it
worked without any errors.

I think the problem has something to do with the pressure since the problem
started during the NPT, but I don't know how exactly to find the problem.
Can anyone guide me please what should I change or how should I start ?

Thanks,
Mohamed

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[gmx-users] Lincs warning and Bond length not finite

[Mohamed Abdelaal]

Hello everyone,

I am simulating  the evaporation of non protein molecules on a graphene
sheet. I am using gromos force field and hence the lincs constrain are set
to all-bonds.  I have done the energy minimization and NVT
successfully without any warnings. During the NPT equilibiration I got
Lincs warning but the NPT equilibiration was completed to the end. During
the md production run, I received lincs warning and Bond length not finite
and sometimes I received " nonbonded interaction between particles is
larger than the table limit 2.437 nm".

I have read that this means that my system is blowing up. Hence, I have
read the Blowing up and diagnosing unstable system  on gromacs website, I
can't recognize  any of the posted issues in my files/simulation and
hence,  I can't decide what exactly is the problem or what should I change
(it seems that my system is well minimized and the temperature and pressure
looks fine). I have added in the below link, the NPT and md logs  and .mdp
files and pictures for the potential energy, Temperature, Pressure and
Density.

https://drive.google.com/drive/folders/1yyUJNg4yXnPfsxZ9gQ4LV5sqRKnJq9rF

I have tried the simulation again with none as  lincs constrains and it
worked without any errors.

I think the problem has something to do with the pressure since the problem
started during the NPT, but I don't know how exactly to find the problem.
Can anyone guide me please what should I change or how should I start ?

Thanks,
Mohamed
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Re: [gmx-users] Lincs warning in free energy calculation (FAISAL NABI)

[Sadaf Rani]

Dear Gromacs users
I am using amber99sb-ildn.ff force field for protein and I used GAFF for
ligand parameterization.
I tried different options e.g using constraint =all bonds as well as
h-bonds. Reducing the time step to 1 fs but still, I could not solve the
problem and get lincs warning production run as below:-
Step 106202, time 212.404 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.035343, max 2.112628 (between atoms 3770 and 3773)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3437   3438   90.02.2392   0.1552  0.1080
   3770   3771   90.00.1045   0.1696  0.1090
   3770   3772   90.02.9369   0.1212  0.1090
   3770   3773   90.00.1043   0.3393  0.1090
Wrote pdb files with previous and current coordinates

Step 106202, time 212.404 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.035038, max 2.096736 (between atoms 3770 and 3773)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3437   3438   90.02.2392   0.1540  0.1080
   3770   3771   90.00.1045   0.1689  0.1090
   3770   3772   90.02.9369   0.1198  0.1090
   3770   3773   90.00.1043   0.3375  0.1090

I would really appreciate your help in fixing this problem I am
facing since long.

Thanks.

Sadaf
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[gmx-users] lincs warning

[Afsane Farhadi]

Sent from Yahoo Mail on Android 
 
   - Forwarded Message - From: "Afsane Farhadi" 
 To: "gromacs.org_gmx-users@maillist.sys.kth.se" 
 Cc:  Sent: Mon, Apr 27, 2020 at 
3:52 PM Subject: lincs warning  Hi users I have two types of molecules ,methane 
and carbondioxide. i optimized them by gaussian calculation and i edited the 
atom name and residue by vim.  I extracted the epsilon and sigma parameter from 
the articles . i generated a box of 500 methane molecules and 62 carbondioxide 
by insert-molecules. I have done energy minimization and its ok (potential 
energy is  -2e+03).when i was running npt.mdp the lincs warning was showed( 
bond rotate more than 30 degree)I need help thanks alot for your quick answers 
.the topology and npt.mdp is:#include "oplsaa.ff/forcefield.itp"

[ atomtypes ]
    CO  C01  12.0110    0.775    A    2.75700E-01   2.33790E-01
    OC  O01  15.99940  -0.388    A    3.03300E-01   6.69120E-01
  opls_801  H801 1.0080 0.125    A    1.48720E-01   0.65688E-01
  opls_803  H803 1.0080 0.125    A    1.48720E-01   0.65688E-01
  opls_804  H804 1.0080 0.125    A    1.48720E-01   0.65688E-01
  opls_800  C800    12.0110    -0.502    A    1.90820E-01   4.57729E-01
  opls_802  H802 1.0080 0.125    A    1.48720E-01   0.65688E-01
[ moleculetype ]
; Name   nrexcl
CH4   3
[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  
 1   opls_800  1  H   C  1    -0.5020    12.0110 
 2   opls_801  1  H   H  1 0.1250 1.0080 
 3   opls_802  1  H   H  1 0.1250 1.0080 
 4   opls_803  1  H   H  1 0.1250 1.0080 
 5   opls_804  1  H   H  1 0.1250 1.0080 
[ bonds ]
    2 1 1  0.1090 138490.400
    3 1 1  0.1090 138490.400
    4 1 1  0.1090 138490.400
    5 1 1  0.1090 138490.400

[ angles ]
;  ai    aj    ak funct    c0    c1    c2    c3 
    2 1 3 1    109.500    146.440
    2 1 4 1    109.500    146.440
    2 1 5 1    109.500    146.440
    3 1 4 1    109.500    146.440
    4 1 5 1    109.500    146.440
    3 1 5 1    109.500    146.440


[ moleculetype ]

; Name   nrexcl
CAR   3

[atoms]

; nr  type resnr residue atom cgnr charge mass

  1   CO    1 CAR    CO   1    0.775  12.0110

  2   OC    1 CAR    OC   1   -0.388  15.9994

  3   OC    1 CAR    OC   1   -0.388  15.9994
  [ bonds ]
  1    2    1   0.11620  844300

  1    3    1   0.11620  844300
  
  
  [angles]
;  ai    aj    ak   funct    c0    c1    c2    
c3   

   2 1 3 1   180 451.9
  
  [system]:

co2 in methane


 [molecules]

  CH4 500
  CAR 62
Sent from Yahoo Mail on Android  
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Re: [gmx-users] lincs warning

[Christian Blau]

Hi Afsane,


This might be an issue with the pressure coupling, depending on the 
compressibility you give for your system and the algorithm that you use 
for pressure coupling you might see quite large fluctuations in 
pressure. One idea might be to use temperature coupling to quickly 
dissipate large energies due to large fluctuations in box size. If 
you're not already using it you could try a robust temperature coupling 
with  v-rescale with tau-t = 0.1, which is usually recommendable. Using 
some steps to carefully anneal your system might help as well. To 
carefully heat your system from 0 to 300K in the first 100ps of the 
simulation you might use "annealing = single annealing-npoints = 2 
annealing-time = 0 100 annealing-temp = 0 300".


Then pressure-pre-equlibrating your system with the Berendsen barostat 
might be helpful, just don't use it for your production run.


Best,

Christian

On 2020-04-25 19:16, Afsane Farhadi wrote:

Hi gromacs users I generated a mixed box of methane and carbondioxide with 
insert-molecules (500 methane+62carbondioxide) . The pdb file of methane and 
carbondioxide are optimized and the energy minimization of mixed gas  is ok 
(potential energy is about -2e+03))but when I want to run a npt run ,the lincs 
warning are showing( bond rotate more than 30 degree).I repeated energy 
minimization but it didn't work right Can any body help me please?

Sent from Yahoo Mail on Android

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Re: [gmx-users] lincs warning

[Yu Du]

Hi Afsane,

You need to provide more details of the simulation, such as how you generated 
the configuration and topology, what force field you used and so on, or we can 
not give you any advice.

Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China.
Zip: 200032, Tel: (86) 021 5492 5275

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Afsane Farhadi 

Sent: Sunday, April 26, 2020 01:16
To: Discussion List for GROMACS Users 
Subject: [gmx-users] lincs warning

Hi gromacs users I generated a mixed box of methane and carbondioxide with 
insert-molecules (500 methane+62carbondioxide) . The pdb file of methane and 
carbondioxide are optimized and the energy minimization of mixed gas  is ok 
(potential energy is about -2e+03))but when I want to run a npt run ,the lincs 
warning are showing( bond rotate more than 30 degree).I repeated energy 
minimization but it didn't work right Can any body help me please?

Sent from Yahoo Mail on Android
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[gmx-users] lincs warning

[Afsane Farhadi]

Hi gromacs users I generated a mixed box of methane and carbondioxide with 
insert-molecules (500 methane+62carbondioxide) . The pdb file of methane and 
carbondioxide are optimized and the energy minimization of mixed gas  is ok 
(potential energy is about -2e+03))but when I want to run a npt run ,the lincs 
warning are showing( bond rotate more than 30 degree).I repeated energy 
minimization but it didn't work right Can any body help me please?

Sent from Yahoo Mail on Android
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Re: [gmx-users] Lincs warning in free energy calculation

[FAISAL NABI]

Check the forcefield you are using is appropriate for your system or  there
might be some problem with the ligand parameters.

On Tue, Mar 24, 2020 at 11:30 AM Sadaf Rani  wrote:

> Dear Gromacs users
> I ran an MD simulation for 3ns and from the last coordinates started a free
> energy calculation for 3ns. My system is well equilibrated but after 710725
> steps I am getting Lincs warning every time as below:-
>
> WARNING: There are no atom pairs for dispersion correction
> starting mdrun 'GROtesk MACabre and Sinister in water'
> 150 steps,   3000.0 ps.
>
> Step 710726, time 1421.45 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.03, max 0.23 (between atoms 5470 and 5472)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>3437   3438   43.80.1080   0.1080  0.1080
>
> Step 710726, time 1421.45 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.03, max 0.21 (between atoms 5470 and 5472)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>3437   3438   43.10.1080   0.1080  0.1080
>
> I have added restraints between atoms of ligand and protein and getting
> Lincs warning between 1 atom included in restraints as below:-
>
> [ bonds ]
> ;i j  type r0A r1A r2AfcAr0B r1B r2B
>  fcB
>   *3437*  790810 0.418   0.418   10.0   0.00.418   0.418   10.0
>   41840.00
>
> [ angle_restraints ]
> ;   aiajakal  typethA  fcAmultA  thB  fcB
>  multB
>   3437  7908  7906  7908   1100.29   0.01 100.29   418.40
> 1
>   7908  3437  3439  *3437*   1146.50   0.01 146.50   418.40
>   1
>
> [ dihedral_restraints ]
> ;   aiajakal   typephiA dphiA  fcAphiB  dphiB
>  fcB
>   7906  7908  *3437*  3439 1156.16   0.00.0156.160.0
>  418.40
>   7907  7906  7908  *3437* 1-56.93   0.00.0-56.930.0
>  418.40
>   7909  *3437*  3430  3435 1131.32   0.00.0131.32 0.0
> 418.40
>
> Can anyone please suggest to me how Should I fix this error? Any help will
> be really appreciated.
>
> Thanks.
>
> Sadaf
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-- 

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C/o Professor Rizwan Hassan Khan
Interdisciplinary Biotechnology Unit,
Aligarh Muslim University, Aligarh, UP, INDIA.
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[gmx-users] Lincs warning in free energy calculation

[Sadaf Rani]

Dear Gromacs users
I ran an MD simulation for 3ns and from the last coordinates started a free
energy calculation for 3ns. My system is well equilibrated but after 710725
steps I am getting Lincs warning every time as below:-

WARNING: There are no atom pairs for dispersion correction
starting mdrun 'GROtesk MACabre and Sinister in water'
150 steps,   3000.0 ps.

Step 710726, time 1421.45 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.03, max 0.23 (between atoms 5470 and 5472)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3437   3438   43.80.1080   0.1080  0.1080

Step 710726, time 1421.45 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.03, max 0.21 (between atoms 5470 and 5472)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3437   3438   43.10.1080   0.1080  0.1080

I have added restraints between atoms of ligand and protein and getting
Lincs warning between 1 atom included in restraints as below:-

[ bonds ]
;i j  type r0A r1A r2AfcAr0B r1B r2B
 fcB
  *3437*  790810 0.418   0.418   10.0   0.00.418   0.418   10.0
  41840.00

[ angle_restraints ]
;   aiajakal  typethA  fcAmultA  thB  fcB
 multB
  3437  7908  7906  7908   1100.29   0.01 100.29   418.40
1
  7908  3437  3439  *3437*   1146.50   0.01 146.50   418.40
  1

[ dihedral_restraints ]
;   aiajakal   typephiA dphiA  fcAphiB  dphiB
 fcB
  7906  7908  *3437*  3439 1156.16   0.00.0156.160.0
 418.40
  7907  7906  7908  *3437* 1-56.93   0.00.0-56.930.0
 418.40
  7909  *3437*  3430  3435 1131.32   0.00.0131.32 0.0
418.40

Can anyone please suggest to me how Should I fix this error? Any help will
be really appreciated.

Thanks.

Sadaf
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Re: [gmx-users] Lincs warning

[Farial Tavakoli]

Dear Mark

Thank you for your reply

I resolved my problem by refining the output ot the tool

Best
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Re: [gmx-users] LINCS warning

[Mark Abraham]

Hi,

I can't tell whether that's a periodicity artefact in your visualization,
or the topology is indeed junk. You will likely need to inspect the output
of the tool that generated it. Rarely do these things "just work."

Mark

On Sun, Nov 11, 2018 at 3:01 AM Farial Tavakoli 
wrote:

> Dear Mark
>
> Thank you for your reply
> I got dt=0.5 ps and run EM and NVT on the ligand in vacuo and got this
> results:
> EM results:
>
> Steepest Descents converged to machine precision in 80 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -3.4145945e+03
> Maximum force =  6.6494578e+04 on atom 81
> Norm of force =  1.0602226e+04
>
> and NVT results:
>
> starting mdrun 'mig'
> 20 steps, 10.0 ps.
> step 199900, remaining wall clock time: 0 s
> Writing final coordinates.
> step 20, remaining wall clock time: 0 s
>Core t (s)   Wall t (s)(%)
>Time:  349.726   87.431  400.0
>  (ns/day)(hour/ns)
> Performance:9.8822.429
> I checked ligand.gro (generated using acpype script) and nvt.gro (generated
> by dt = 0.5) files by VMD and noticed the phosphate groups were not
> bound to tyrosine residues in ligand.gro and there was bad contacts in them
> in nvt.gro . Is it because of VMD software or there is a problem in
> converting files?
> If it is needed I will send you my files to you.
>
> Thanks in advance
> Farial
> --
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Re: [gmx-users] LINCS warning

[Farial Tavakoli]

Dear Mark

Thank you for your reply
I got dt=0.5 ps and run EM and NVT on the ligand in vacuo and got this
results:
EM results:

Steepest Descents converged to machine precision in 80 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -3.4145945e+03
Maximum force =  6.6494578e+04 on atom 81
Norm of force =  1.0602226e+04

and NVT results:

starting mdrun 'mig'
20 steps, 10.0 ps.
step 199900, remaining wall clock time: 0 s
Writing final coordinates.
step 20, remaining wall clock time: 0 s
   Core t (s)   Wall t (s)(%)
   Time:  349.726   87.431  400.0
 (ns/day)(hour/ns)
Performance:9.8822.429
I checked ligand.gro (generated using acpype script) and nvt.gro (generated
by dt = 0.5) files by VMD and noticed the phosphate groups were not
bound to tyrosine residues in ligand.gro and there was bad contacts in them
in nvt.gro . Is it because of VMD software or there is a problem in
converting files?
If it is needed I will send you my files to you.

Thanks in advance
Farial
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Re: [gmx-users] LINCS warning

[Mark Abraham]

Hi,

That tends to suggest either your ligand conformation or ligand parameters
are not appropriate. What happens with ligand in vacuo with EM and then NVE
with a very small time step, e.g. 0.5 ps?

Mark

On Sat, Nov 10, 2018 at 10:50 AM Farial Tavakoli 
wrote:

> Dear gromacs users
>
> I am trying to simulate a complex, including a protein and a peptidec
> ligand with 2 phosphotyrosine residues.
> The protein topology was generated using amber99sb.ff in gromacs and the
> ligand topology was generated using ff99sb in amber tools 16, then the
> .inpcrd and .prmtop files were converted to .gmx and .top files using
> acpype python script.
> *python acpype.py -p prmtop -x inpcrd*
> .itp file was created by removing  header and footer of .top file.
> Then .gro and .top files were modified according to the tutorial in
> gromacs.
> I tryed to minimize the complex , but it stoped before 100 steps :
>
>
>
>
>
> *Steepest Descents converged to machine precision in 80 steps,but did not
> reach the requested Fmax < 1000.Potential Energy  = -6.5639856e+05Maximum
> force =  7.0647156e+04 on atom 5256Norm of force =  5.8775842e+02*
>
> and when I run NVT simulation , faced to LINCS warning:
>
>
>
>
>
>
>
>
>
>
> *starting mdrun 'Protein in water'20 steps,400.0 ps.step 0Step 5,
> time 0.01 (ps)  LINCS WARNINGrelative constraint deviation after LINCS:rms
> 0.016999, max 0.734404 (between atoms 5258 and 5261)bonds that rotated more
> than 30 degrees: atom 1 atom 2  angle  previous, current, constraint
> length   5258   5261   90.00.0960   0.1665  0.0960   5283   5286
> 90.00.0960   0.1425  0.0960Wrote pdb files with previous and
> current coordinates*
> I separated my complex in to protein and ligand and simulated the protein
> alone in the TIP3P water model. that was stable. then, simulated the ligand
> in vacuo and faced with LINCS warning.
> Both force fields that were used to generate topologies were AMBER99sb, Is
> it possible its because of .mdp files which I used?
> Would you please reply and advice me how I can resolve this problem?
>
> best regards
> Farial
>
> the em.mdp file:
> ; minim.mdp - used as input into grompp to generate em.tpr
> integrator  = steep
> emtol   = 1000.0
> emstep  = 0.01
> nsteps  = 5
> nstlist = 1
> cutoff-scheme   = Verlet
> ns_type = grid
> coulombtype = PME
> rcoulomb= 1.0
> rvdw= 1.0
> pbc = xyz
>
> nvt.mdp file:
> title   = AMBER  NVT equilibration
> define  = -DPOSRES  ; position restrain the protein
> ; Run parameters
> integrator  = md
> nsteps  = 20 ; 2 * 20 = 400 ps
> dt  = 0.002
> ; Output control
> nstxout = 500
> nstvout = 500
> nstenergy   = 500
> nstlog  = 500
> ; Bond parameters
> continuation= no
> constraint_algorithm= lincs
> constraints = h-bonds
> lincs_iter  = 1
> lincs_order = 4
> ; Nonbonded settings
> cutoff-scheme   = Verlet
> ns_type = grid
> nstlist = 10
> rcoulomb= 1.0
> rvdw= 1.0
> ; Electrostatics
> coulombtype = PME
> pme_order   = 4
> fourierspacing  = 0.16
> ; Temperature coupling is on
> tcoupl  = V-rescale
> tc-grps = Protein Non-Protein
> tau_t   = 0.1 0.1
> ref_t   = 300 300
> ; Pressure coupling is off
> pcoupl  = no
> ; Periodic boundary conditions
> pbc = xyz
> ; Velocity generation
> gen_vel = yes
> gen_temp= 300
> gen_seed= -1
> --
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>
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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>
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[gmx-users] LINCS warning

[Farial Tavakoli]

Dear gromacs users

I am trying to simulate a complex, including a protein and a peptidec
ligand with 2 phosphotyrosine residues.
The protein topology was generated using amber99sb.ff in gromacs and the
ligand topology was generated using ff99sb in amber tools 16, then the
.inpcrd and .prmtop files were converted to .gmx and .top files using
acpype python script.
*python acpype.py -p prmtop -x inpcrd*
.itp file was created by removing  header and footer of .top file.
Then .gro and .top files were modified according to the tutorial in
gromacs.
I tryed to minimize the complex , but it stoped before 100 steps :





*Steepest Descents converged to machine precision in 80 steps,but did not
reach the requested Fmax < 1000.Potential Energy  = -6.5639856e+05Maximum
force =  7.0647156e+04 on atom 5256Norm of force =  5.8775842e+02*

and when I run NVT simulation , faced to LINCS warning:










*starting mdrun 'Protein in water'20 steps,400.0 ps.step 0Step 5,
time 0.01 (ps)  LINCS WARNINGrelative constraint deviation after LINCS:rms
0.016999, max 0.734404 (between atoms 5258 and 5261)bonds that rotated more
than 30 degrees: atom 1 atom 2  angle  previous, current, constraint
length   5258   5261   90.00.0960   0.1665  0.0960   5283   5286
90.00.0960   0.1425  0.0960Wrote pdb files with previous and
current coordinates*
I separated my complex in to protein and ligand and simulated the protein
alone in the TIP3P water model. that was stable. then, simulated the ligand
in vacuo and faced with LINCS warning.
Both force fields that were used to generate topologies were AMBER99sb, Is
it possible its because of .mdp files which I used?
Would you please reply and advice me how I can resolve this problem?

best regards
Farial

the em.mdp file:
; minim.mdp - used as input into grompp to generate em.tpr
integrator  = steep
emtol   = 1000.0
emstep  = 0.01
nsteps  = 5
nstlist = 1
cutoff-scheme   = Verlet
ns_type = grid
coulombtype = PME
rcoulomb= 1.0
rvdw= 1.0
pbc = xyz

nvt.mdp file:
title   = AMBER  NVT equilibration
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md
nsteps  = 20 ; 2 * 20 = 400 ps
dt  = 0.002
; Output control
nstxout = 500
nstvout = 500
nstenergy   = 500
nstlog  = 500
; Bond parameters
continuation= no
constraint_algorithm= lincs
constraints = h-bonds
lincs_iter  = 1
lincs_order = 4
; Nonbonded settings
cutoff-scheme   = Verlet
ns_type = grid
nstlist = 10
rcoulomb= 1.0
rvdw= 1.0
; Electrostatics
coulombtype = PME
pme_order   = 4
fourierspacing  = 0.16
; Temperature coupling is on
tcoupl  = V-rescale
tc-grps = Protein Non-Protein
tau_t   = 0.1 0.1
ref_t   = 300 300
; Pressure coupling is off
pcoupl  = no
; Periodic boundary conditions
pbc = xyz
; Velocity generation
gen_vel = yes
gen_temp= 300
gen_seed= -1
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Re: [gmx-users] LINCS WARNING during EPM2 CO2 Simulation

[Mark Abraham]

Hi,

Simplify things until you identify the problematic part. Eg do one CO2
molecule first.

Mark

On Thu, 19 Oct 2017 03:16 Pimo Oni  wrote:

> Dear community members,
>
> Recently I'm using GMX 5.1.4 to simulate EPM2 CO2 with virtual sites, while
> I met continual LINCS WARNING. I've been struggling for more than week but
> make no progress in fixing it.. : (
>
> Here attach my pdb, top, and mdp files below.
> I would much appreciate any tip & comments.
>
> Thanks
> Pimo
>
> -
>
> ***command used***
>
> gmx_d insert-molecules -f co2EPM2.pdb -ci co2EPM2.pdb -o testco2.pdb -box 5
> 5 5 -nmol 999
>
> gmx_d grompp -f em.mdp -po testco2em.mdp -c testco2.pdb -p co2EPM2.top -o
> testco2em.tpr
>
> gmx_d mdrun -s testco2em.tpr -deffnm testco2em
>
> ***error***
> Step 12, time 0.012 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.00, max 0.00 (between atoms 2201 and 2202)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>  21 22   48.50.1978   0.1978  0.1978
>2496   2497   47.70.1978   0.1978  0.1978
>2496   2497   47.70.1978   0.1978  0.1978
>2496   2497   47.70.1978   0.1978  0.1978
>2496   2497   47.70.1978   0.1978  0.1978
>
> ***co2EPM2.pdb***
> TITLE CO2 with dummy masses
> REMARKTHIS IS A SIMULATION BOX
> CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1   1
> MODEL1
> ATOM  1  M1  CO2 1   0.171   0.000   0.000  1.00  0.00
>
> ATOM  2  M2  CO2 1   2.149   0.000   0.000  1.00  0.00
>
> ATOM  3  C   CO2 1   1.160   0.000   0.000  1.00  0.00
>
> ATOM  4  O1  CO2 1   0.000   0.000   0.000  1.00  0.00
>
> ATOM  5  O2  CO2 1   2.320   0.000   0.000  1.00  0.00
>
> TER
> ENDMDL
>
> ***co2EPM2.top***
> [ defaults ]
> ; nbfunc  comb-rule  gen-pairs  fudgeLJ  fudgeQQ
>   1   2  no 1.0  1.0
>
>  [ atomtypes ]
> ; type  mass charge  ptype sigma(nm) epsilon(kJ/M)
>   M 22.00475  0. A 0.0   0.
>   C  0.0  0.6512 V 0.27570   0.2339
>   O  0.0 -0.3256 V 0.30330   0.6694
>
>
> [ moleculetype ]
> ; name nrexcl
>   CO2  2
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge  mass
>   1  M1 CO2M1   1 0. 22.00475
>   2  M1 CO2M2   1 0. 22.00475
>   3  C1 CO2C1 0.6512  0.0
>   4  O1 CO2O1   1-0.3256  0.0
>   5  O1 CO2O2   1-0.3256  0.0
>
> [ constraints ]
> ; ai aj funct distance
>   1  2  1 0.1978252
>
> [ virtual_sites2 ]
> ; ai aj ak funct a
>   3  1  2  1 0.5000
>   4  1  2  1 1.086376
>   5  2  1  1 1.086376
>
> [ exclusions ]
> 3 4 5
> 4 5 3
> 5 4 3
>
> [ system ]
> CO2EPM2
>
> [ molecules ]
> ; name nmol
>   CO2  1000
>
> ***em.mdp***
> define   =
>
> ; RUN CONTROL PARAMETERS
> integrator   = steep
> tinit= 0
> dt   = 0.001
> nsteps   = -1
> init_step= 0
> simulation_part  = 1
> comm-mode= Linear
> nstcomm  = 100
> comm-grps=
>
> emtol= 10.0
> emstep   = 0.01
> niter= 20
> fcstep   = 0
> nstcgsteep   = 1000
> nbfgscorr= 10
> energygrps   = system
>
> cutoff-scheme= Verlet
> nstlist  = 10
> ns_type  = grid
> pbc  = xyz
> periodic_molecules   = no
> verlet-buffer-tolerance  = -1
> rlist= 1.5
> rlistlong= -1
> nstcalclr= -1
>
> ; Method for doing electrostatics
> coulombtype  = PME
> coulomb-modifier = Potential-shift-Verlet
> rcoulomb-switch  = 0
> rcoulomb = 1.5
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r= 1
> epsilon_rf   = 1
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> vdw-modifier = Potential-shift-Verlet
> ; cut-off lengths
> rvdw-switch  = 0
> rvdw = 1.5
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = no
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension  = 1
> ; Separate tables between energy group pairs
> energygrp-table  =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing   = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> ; EWALD/PME/PPPM parameters
> pme_order= 4
> ewald_rtol   = 1e-05
> ewald-rtol-lj= 0.001
> lj-pme-comb-rule 

[gmx-users] LINCS WARNING during EPM2 CO2 Simulation

[Pimo Oni]

Dear community members,

Recently I'm using GMX 5.1.4 to simulate EPM2 CO2 with virtual sites, while
I met continual LINCS WARNING. I've been struggling for more than week but
make no progress in fixing it.. : (

Here attach my pdb, top, and mdp files below.
I would much appreciate any tip & comments.

Thanks
Pimo

-

***command used***

gmx_d insert-molecules -f co2EPM2.pdb -ci co2EPM2.pdb -o testco2.pdb -box 5
5 5 -nmol 999

gmx_d grompp -f em.mdp -po testco2em.mdp -c testco2.pdb -p co2EPM2.top -o
testco2em.tpr

gmx_d mdrun -s testco2em.tpr -deffnm testco2em

***error***
Step 12, time 0.012 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.00, max 0.00 (between atoms 2201 and 2202)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 21 22   48.50.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978
   2496   2497   47.70.1978   0.1978  0.1978

***co2EPM2.pdb***
TITLE CO2 with dummy masses
REMARKTHIS IS A SIMULATION BOX
CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  M1  CO2 1   0.171   0.000   0.000  1.00  0.00

ATOM  2  M2  CO2 1   2.149   0.000   0.000  1.00  0.00

ATOM  3  C   CO2 1   1.160   0.000   0.000  1.00  0.00

ATOM  4  O1  CO2 1   0.000   0.000   0.000  1.00  0.00

ATOM  5  O2  CO2 1   2.320   0.000   0.000  1.00  0.00

TER
ENDMDL

***co2EPM2.top***
[ defaults ]
; nbfunc  comb-rule  gen-pairs  fudgeLJ  fudgeQQ
  1   2  no 1.0  1.0

 [ atomtypes ]
; type  mass charge  ptype sigma(nm) epsilon(kJ/M)
  M 22.00475  0. A 0.0   0.
  C  0.0  0.6512 V 0.27570   0.2339
  O  0.0 -0.3256 V 0.30330   0.6694


[ moleculetype ]
; name nrexcl
  CO2  2

[ atoms ]
; nr type resnr residu atom cgnr charge  mass
  1  M1 CO2M1   1 0. 22.00475
  2  M1 CO2M2   1 0. 22.00475
  3  C1 CO2C1 0.6512  0.0
  4  O1 CO2O1   1-0.3256  0.0
  5  O1 CO2O2   1-0.3256  0.0

[ constraints ]
; ai aj funct distance
  1  2  1 0.1978252

[ virtual_sites2 ]
; ai aj ak funct a
  3  1  2  1 0.5000
  4  1  2  1 1.086376
  5  2  1  1 1.086376

[ exclusions ]
3 4 5
4 5 3
5 4 3

[ system ]
CO2EPM2

[ molecules ]
; name nmol
  CO2  1000

***em.mdp***
define   =

; RUN CONTROL PARAMETERS
integrator   = steep
tinit= 0
dt   = 0.001
nsteps   = -1
init_step= 0
simulation_part  = 1
comm-mode= Linear
nstcomm  = 100
comm-grps=

emtol= 10.0
emstep   = 0.01
niter= 20
fcstep   = 0
nstcgsteep   = 1000
nbfgscorr= 10
energygrps   = system

cutoff-scheme= Verlet
nstlist  = 10
ns_type  = grid
pbc  = xyz
periodic_molecules   = no
verlet-buffer-tolerance  = -1
rlist= 1.5
rlistlong= -1
nstcalclr= -1

; Method for doing electrostatics
coulombtype  = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch  = 0
rcoulomb = 1.5
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
; cut-off lengths
rvdw-switch  = 0
rvdw = 1.5
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = no
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Separate tables between energy group pairs
energygrp-table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald-rtol-lj= 0.001
lj-pme-comb-rule = Geometric
ewald_geometry   = 3d
epsilon_surface  = 0

; Temperature coupling
tcoupl   = Berendsen
nsttcouple   = -1
nh-chain-length  = 10
print-nose-hoover-chain-variables = no
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau-t= 1
ref-t= 300
; pressure coupling
Pcoupl   = no

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

[Justin Lemkul]

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  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

  193194   51.70.1100   0.1100  0.1100

54409  54410   32.30.1100   0.1100  0.1100

On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren 
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.war...@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  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  = 5

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  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 

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

[Ali Ahmed]

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
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  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
>>
>>  193194   51.70.1100   0.1100  0.1100
>>
>>54409  54410   32.30.1100   0.1100  0.1100
>>
>> On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren 
>> 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.war...@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  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  = 5

 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 
 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 

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

[Justin Lemkul]

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

 193194   51.70.1100   0.1100  0.1100

   54409  54410   32.30.1100   0.1100  0.1100

On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren 
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.war...@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  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  = 5

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 
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  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.abra...@gmail.com>

wrote:


Hi,

Did you get any warnings from grompp?

Mark

On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed 

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_typemasscharge   ptype  sigma

epsilon


   OP   OP0.000   0.000A  0.330

0.3062

;

nitrogen

   M  M  0.000   0.000V  0.000

0.000

;

virtual site







[ moleculetype ]

; name  nrexcl

N2 2



[ atoms ]

;   nr   typeresnr residue  atom   cgnr   charge mass

  1 OP  1N2 N1  1-0.482

14.0067


  2 M 1N2 M1  1 0.964 0.000

  3 OP   1N2 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

REMARKTHIS IS A SIMULATION BOX

MODEL1

COMPNDUNNAMED

AUTHORGENERATED BY OPEN BABEL 2.3.2

CRYST1   50.000   50.000   50.000  

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

[Ali Ahmed]

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

193194   51.70.1100   0.1100  0.1100

  54409  54410   32.30.1100   0.1100  0.1100

On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren 
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.war...@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  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  = 5
> >
> > 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 
> > 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  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.abra...@gmail.com>
> >> > wrote:
> >> >
> >> > > Hi,
> >> > >
> >> > > Did you get any warnings from grompp?
> >> > >
> >> > > Mark
> >> > >
> >> > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed 
> 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_typemasscharge   ptype  sigma
> >> epsilon
> >> > > >
> >> > > >   OP   OP0.000   0.000A  0.330
> >> 0.3062
> >> > ;
> >> > > > nitrogen
> >> > > >
> >> > > >   M  M  0.000   0.000V  0.000
> >> > 0.000
> >> > > ;
> >> > > > virtual site
> >> > > >
> >> > > >
> >> > > > 
> >> > > 
> >> > > >
> >> > > > [ moleculetype ]
> >> > > >
> >> > > > ; name  nrexcl
> >> > > >
> >> > > > N2 2
> >> > > >
> >> > > >
> >> > > >
> >> > > > [ atoms ]
> >> > > >
> >> > > > ;   nr   typeresnr residue  atom   cgnr   charge mass
> >> > > >
> >> > > >  1 OP  1N2 N1  1-0.482
> 14.0067
> >> > > >
> >> > > >  2 M 1N2 M1  1 0.964 0.000
> >> > > >
> >> > > >   

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

[Dallas Warren]

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.war...@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  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  = 5
>
> 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 
> 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  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 
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > Did you get any warnings from grompp?
>> > >
>> > > Mark
>> > >
>> > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed  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_typemasscharge   ptype  sigma
>> epsilon
>> > > >
>> > > >   OP   OP0.000   0.000A  0.330
>> 0.3062
>> > ;
>> > > > nitrogen
>> > > >
>> > > >   M  M  0.000   0.000V  0.000
>> > 0.000
>> > > ;
>> > > > virtual site
>> > > >
>> > > >
>> > > > 
>> > > 
>> > > >
>> > > > [ moleculetype ]
>> > > >
>> > > > ; name  nrexcl
>> > > >
>> > > > N2 2
>> > > >
>> > > >
>> > > >
>> > > > [ atoms ]
>> > > >
>> > > > ;   nr   typeresnr residue  atom   cgnr   charge mass
>> > > >
>> > > >  1 OP  1N2 N1  1-0.482  14.0067
>> > > >
>> > > >  2 M 1N2 M1  1 0.964 0.000
>> > > >
>> > > >  3 OP   1N2 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
>> > > >
>> > > > REMARKTHIS IS A SIMULATION BOX
>> > > >
>> > > > MODEL1
>> > > >
>> > > > COMPNDUNNAMED
>> > > >
>> > > > AUTHORGENERATED BY OPEN BABEL 2.3.2
>> > > >
>> > > > CRYST1   50.000   50.000   50.000  90.00  

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

[Ali Ahmed]

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  = 5

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 
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  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 
> > wrote:
> >
> > > Hi,
> > >
> > > Did you get any warnings from grompp?
> > >
> > > Mark
> > >
> > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed  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_typemasscharge   ptype  sigma
> epsilon
> > > >
> > > >   OP   OP0.000   0.000A  0.330
> 0.3062
> > ;
> > > > nitrogen
> > > >
> > > >   M  M  0.000   0.000V  0.000
> > 0.000
> > > ;
> > > > virtual site
> > > >
> > > >
> > > > 
> > > 
> > > >
> > > > [ moleculetype ]
> > > >
> > > > ; name  nrexcl
> > > >
> > > > N2 2
> > > >
> > > >
> > > >
> > > > [ atoms ]
> > > >
> > > > ;   nr   typeresnr residue  atom   cgnr   charge mass
> > > >
> > > >  1 OP  1N2 N1  1-0.482  14.0067
> > > >
> > > >  2 M 1N2 M1  1 0.964 0.000
> > > >
> > > >  3 OP   1N2 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
> > > >
> > > > REMARKTHIS IS A SIMULATION BOX
> > > >
> > > > MODEL1
> > > >
> > > > COMPNDUNNAMED
> > > >
> > > > AUTHORGENERATED 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
> > > >
> > > > CONECT13
> > > >
> > > > CONECT31
> > > >
> > > > MASTER00000000303
> 0
> > > >
> > > > END0
> > > >
> > > > 
> > > > -
> > > > Thank you
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > 

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

[Ali Ahmed]

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 
wrote:

> Hi,
>
> Did you get any warnings from grompp?
>
> Mark
>
> On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed  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_typemasscharge   ptype  sigma  epsilon
> >
> >   OP   OP0.000   0.000A  0.330  0.3062 ;
> > nitrogen
> >
> >   M  M  0.000   0.000V  0.000  0.000
> ;
> > virtual site
> >
> >
> > 
> 
> >
> > [ moleculetype ]
> >
> > ; name  nrexcl
> >
> > N2 2
> >
> >
> >
> > [ atoms ]
> >
> > ;   nr   typeresnr residue  atom   cgnr   charge mass
> >
> >  1 OP  1N2 N1  1-0.482  14.0067
> >
> >  2 M 1N2 M1  1 0.964 0.000
> >
> >  3 OP   1N2 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
> >
> > REMARKTHIS IS A SIMULATION BOX
> >
> > MODEL1
> >
> > COMPNDUNNAMED
> >
> > AUTHORGENERATED 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
> >
> > CONECT13
> >
> > CONECT31
> >
> > MASTER000000003030
> >
> > END0
> >
> > 
> > -
> > Thank you
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

[Mark Abraham]

Hi,

Did you get any warnings from grompp?

Mark

On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed  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_typemasscharge   ptype  sigma  epsilon
>
>   OP   OP0.000   0.000A  0.330  0.3062 ;
> nitrogen
>
>   M  M  0.000   0.000V  0.000  0.000 ;
> virtual site
>
>
> 
>
> [ moleculetype ]
>
> ; name  nrexcl
>
> N2 2
>
>
>
> [ atoms ]
>
> ;   nr   typeresnr residue  atom   cgnr   charge mass
>
>  1 OP  1N2 N1  1-0.482  14.0067
>
>  2 M 1N2 M1  1 0.964 0.000
>
>  3 OP   1N2 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
>
> REMARKTHIS IS A SIMULATION BOX
>
> MODEL1
>
> COMPNDUNNAMED
>
> AUTHORGENERATED 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
>
> CONECT13
>
> CONECT31
>
> MASTER000000003030
>
> END0
>
> 
> -
> Thank you
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

[Ali Ahmed]

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_typemasscharge   ptype  sigma  epsilon

  OP   OP0.000   0.000A  0.330  0.3062 ;
nitrogen

  M  M  0.000   0.000V  0.000  0.000 ;
virtual site



[ moleculetype ]

; name  nrexcl

N2 2



[ atoms ]

;   nr   typeresnr residue  atom   cgnr   charge mass

 1 OP  1N2 N1  1-0.482  14.0067

 2 M 1N2 M1  1 0.964 0.000

 3 OP   1N2 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

REMARKTHIS IS A SIMULATION BOX

MODEL1

COMPNDUNNAMED

AUTHORGENERATED 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

CONECT13

CONECT31

MASTER000000003030

END0


-
Thank you
-- 
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Re: [gmx-users] LINCS warning during constrained md

[edesantis]

Dear Mark,
I understand your point,
but I've used the Martini-backmapping protocol written in the initram.sh 
wrapper found in Martini documentation 
(https://github.com/Tsjerk/MartiniTools/blob/master/initram.sh), so it 
seems to me quite weird that it was not working in the proper manner.



an other problem is that I've to convert some thousands of structure 
extracted from the martini trajectory,
I thought that this kind of conversion doesn't require to much effort, 
so for this reason I thought that the posres flag was useful to limit 
the computational time... maybe I'm wrong


Can I avoid to use constrained bonds and use only posres? what do you 
think about?




in addition, for you, how many steps of md have I to perform to do this 
kind of equilibration? have I to look necessarily at the rmsd in each 
trajectory? I'd like to have a robust protocol to do all the conversions 
in an automatic way...


thank you again for your suggestions
regards,
Emiliano



On 2017-07-12 17:23, Mark Abraham wrote:

Hi,

I would avoid using the combination of position restraints and 
constrained
bonds with an input structure that is not necessarily consistent with 
the

constraints. That's a recipe for large forces. I wouldn't use position
restraints in such a process unless I had some reason to believe that 
my
starting structure was special *and* saw a large deformation if I 
didn't
use the restraints. If I saw the deformation, I would wonder why I 
thought

it was special.

If you're trying to relax a thing, let it relax. :-) If something 
strange
happens, consider that when it has happened. Obviously that means you 
want
to look at what happens when you did your equilibration, but you were 
going

to do that anyway. Right? ;-)

Mark

On Wed, Jul 12, 2017 at 5:17 PM edesantis  
wrote:



hi,

I've seen with vmd the gro file generated after the transformation, 
and

after the 2 steps of minimization,
it seems that they have no problem,
while if I see the step_n.pdb file generated before the crash, there 
are

some atoms far away from the rest of the protein, while this is not
happening if I comment the restrains part


do you understand why??

thank you again,
Emiliano



On 2017-07-12 16:29, Mark Abraham wrote:
> Hi,
>
> Those are all good things, but have you actually got out a molecular
> viewer
> and looked at the input and output of your resolution conversion?
>
> Mark
>
> On Wed, Jul 12, 2017 at 4:25 PM edesantis 
> wrote:
>
>> Hi,
>> thanks for the prompt answer,
>>
>>
>> I've found the same problem even if I try to convert the coarse
>> grained
>> pdb obtained from martinize.py, so in that case it should be not a
>> problem to have the conversion, for this reason I though it is a
>> methodological problem...
>>
>> I've seen the blowing-up issues , but I think:
>> - the timestep is enough small  (0.0002)
>> -the system should be enough minimized via the previous steps (in fact
>> the sd converged to the machine precision in both cases, actually the
>> potential energy is ~10^5, but I don't know how to reduce it, I tried
>> a
>> cg after the sd, but the proble is still there)
>> -there in not any pressure coupling
>> -I've tried a different temperature coupling (berensden, nose-hoover)
>> and it doesn't work
>> - the md stops at the first step, so there is not any .edr file
>> produced
>> to be looked at
>>
>>
>>
>> I don't know what else to do...
>>
>> maybe, do you know another conversion protocol to use??
>>
>>
>> thank you again
>> Emiliano
>>
>> On 2017-07-12 15:11, Mark Abraham wrote:
>> > Hi,
>> >
>> > Sounds like you might be
>> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up because
the
>> > conversion doesn't work for your configuration. You should start by
>> > doing a
>> > visual check of the configuration for sanity, then follow the advice
in
>> > that link.
>> >
>> > Mark
>> >
>> > On Wed, Jul 12, 2017 at 3:04 PM edesantis 
>> > wrote:
>> >
>> >> dear all,
>> >>
>> >> I am facing a problem with the conversion from Martini CG
>> >> representation
>> >> to All-atomistic one.
>> >>
>> >> I am using the initram.sh wrapper around the backward.py.
>> >>
>> >> There is a LINCS warning problem when the energy relaxation is
>> >> performed
>> >> using position restrained md
>> >> (I've also tried to run grompp and mdrun commands directly from the
>> >> terminal and the error persists, so it is not a wrapper problem).
>> >>
>> >> this is the .mdp file generated by the script:
>> >>
>> >> "define   = -DPOSRES
>> >> integrator   = md
>> >> nsteps   = 500
>> >> dt   = 0.0002
>> >> pbc  = xyz
>> >>
>> >> rcoulomb = 0.9
>> >> rlist= 0.9
>> >> rvdw = 0.9
>> >>
>> >> tcoupl   = v-rescale
>> >> ref_t= 200
>> >> tau_t= 0.1
>> >> 

Re: [gmx-users] LINCS warning during constrained md

[Mark Abraham]

Hi,

I would avoid using the combination of position restraints and constrained
bonds with an input structure that is not necessarily consistent with the
constraints. That's a recipe for large forces. I wouldn't use position
restraints in such a process unless I had some reason to believe that my
starting structure was special *and* saw a large deformation if I didn't
use the restraints. If I saw the deformation, I would wonder why I thought
it was special.

If you're trying to relax a thing, let it relax. :-) If something strange
happens, consider that when it has happened. Obviously that means you want
to look at what happens when you did your equilibration, but you were going
to do that anyway. Right? ;-)

Mark

On Wed, Jul 12, 2017 at 5:17 PM edesantis  wrote:

> hi,
>
> I've seen with vmd the gro file generated after the transformation, and
> after the 2 steps of minimization,
> it seems that they have no problem,
> while if I see the step_n.pdb file generated before the crash, there are
> some atoms far away from the rest of the protein, while this is not
> happening if I comment the restrains part
>
>
> do you understand why??
>
> thank you again,
> Emiliano
>
>
>
> On 2017-07-12 16:29, Mark Abraham wrote:
> > Hi,
> >
> > Those are all good things, but have you actually got out a molecular
> > viewer
> > and looked at the input and output of your resolution conversion?
> >
> > Mark
> >
> > On Wed, Jul 12, 2017 at 4:25 PM edesantis 
> > wrote:
> >
> >> Hi,
> >> thanks for the prompt answer,
> >>
> >>
> >> I've found the same problem even if I try to convert the coarse
> >> grained
> >> pdb obtained from martinize.py, so in that case it should be not a
> >> problem to have the conversion, for this reason I though it is a
> >> methodological problem...
> >>
> >> I've seen the blowing-up issues , but I think:
> >> - the timestep is enough small  (0.0002)
> >> -the system should be enough minimized via the previous steps (in fact
> >> the sd converged to the machine precision in both cases, actually the
> >> potential energy is ~10^5, but I don't know how to reduce it, I tried
> >> a
> >> cg after the sd, but the proble is still there)
> >> -there in not any pressure coupling
> >> -I've tried a different temperature coupling (berensden, nose-hoover)
> >> and it doesn't work
> >> - the md stops at the first step, so there is not any .edr file
> >> produced
> >> to be looked at
> >>
> >>
> >>
> >> I don't know what else to do...
> >>
> >> maybe, do you know another conversion protocol to use??
> >>
> >>
> >> thank you again
> >> Emiliano
> >>
> >> On 2017-07-12 15:11, Mark Abraham wrote:
> >> > Hi,
> >> >
> >> > Sounds like you might be
> >> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up because
> the
> >> > conversion doesn't work for your configuration. You should start by
> >> > doing a
> >> > visual check of the configuration for sanity, then follow the advice
> in
> >> > that link.
> >> >
> >> > Mark
> >> >
> >> > On Wed, Jul 12, 2017 at 3:04 PM edesantis 
> >> > wrote:
> >> >
> >> >> dear all,
> >> >>
> >> >> I am facing a problem with the conversion from Martini CG
> >> >> representation
> >> >> to All-atomistic one.
> >> >>
> >> >> I am using the initram.sh wrapper around the backward.py.
> >> >>
> >> >> There is a LINCS warning problem when the energy relaxation is
> >> >> performed
> >> >> using position restrained md
> >> >> (I've also tried to run grompp and mdrun commands directly from the
> >> >> terminal and the error persists, so it is not a wrapper problem).
> >> >>
> >> >> this is the .mdp file generated by the script:
> >> >>
> >> >> "define   = -DPOSRES
> >> >> integrator   = md
> >> >> nsteps   = 500
> >> >> dt   = 0.0002
> >> >> pbc  = xyz
> >> >>
> >> >> rcoulomb = 0.9
> >> >> rlist= 0.9
> >> >> rvdw = 0.9
> >> >>
> >> >> tcoupl   = v-rescale
> >> >> ref_t= 200
> >> >> tau_t= 0.1
> >> >> tc_grps  = System
> >> >>
> >> >> gen_vel  = yes
> >> >> gen_temp = 300
> >> >>
> >> >> constraints  = all-bonds "
> >> >>
> >> >>
> >> >> this is the error I found in the .log file:
> >> >>
> >> >> "Fatal error:
> >> >> Too many LINCS warnings (1034)
> >> >> If you know what you are doing you can adjust the lincs warning
> >> >> threshold in your mdp file
> >> >> or set the environment variable GMX_MAXCONSTRWARN to -1,
> >> >> but normally it is better to fix the problem "
> >> >>
> >> >> I tired to comment the constrains part and all is working, but since
> >> >> the
> >> >> structure should not be altered too much, I think the constraints are
> >> >> required (if I constrain only the h-bonds, it is also working).
> >> >>
> >> >> I've also added to the .mdp 

Re: [gmx-users] LINCS warning during constrained md

[edesantis]

hi,

I've seen with vmd the gro file generated after the transformation, and 
after the 2 steps of minimization,

it seems that they have no problem,
while if I see the step_n.pdb file generated before the crash, there are 
some atoms far away from the rest of the protein, while this is not 
happening if I comment the restrains part



do you understand why??

thank you again,
Emiliano



On 2017-07-12 16:29, Mark Abraham wrote:

Hi,

Those are all good things, but have you actually got out a molecular 
viewer

and looked at the input and output of your resolution conversion?

Mark

On Wed, Jul 12, 2017 at 4:25 PM edesantis  
wrote:



Hi,
thanks for the prompt answer,


I've found the same problem even if I try to convert the coarse 
grained

pdb obtained from martinize.py, so in that case it should be not a
problem to have the conversion, for this reason I though it is a
methodological problem...

I've seen the blowing-up issues , but I think:
- the timestep is enough small  (0.0002)
-the system should be enough minimized via the previous steps (in fact
the sd converged to the machine precision in both cases, actually the
potential energy is ~10^5, but I don't know how to reduce it, I tried 
a

cg after the sd, but the proble is still there)
-there in not any pressure coupling
-I've tried a different temperature coupling (berensden, nose-hoover)
and it doesn't work
- the md stops at the first step, so there is not any .edr file 
produced

to be looked at



I don't know what else to do...

maybe, do you know another conversion protocol to use??


thank you again
Emiliano

On 2017-07-12 15:11, Mark Abraham wrote:
> Hi,
>
> Sounds like you might be
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
> conversion doesn't work for your configuration. You should start by
> doing a
> visual check of the configuration for sanity, then follow the advice in
> that link.
>
> Mark
>
> On Wed, Jul 12, 2017 at 3:04 PM edesantis 
> wrote:
>
>> dear all,
>>
>> I am facing a problem with the conversion from Martini CG
>> representation
>> to All-atomistic one.
>>
>> I am using the initram.sh wrapper around the backward.py.
>>
>> There is a LINCS warning problem when the energy relaxation is
>> performed
>> using position restrained md
>> (I've also tried to run grompp and mdrun commands directly from the
>> terminal and the error persists, so it is not a wrapper problem).
>>
>> this is the .mdp file generated by the script:
>>
>> "define   = -DPOSRES
>> integrator   = md
>> nsteps   = 500
>> dt   = 0.0002
>> pbc  = xyz
>>
>> rcoulomb = 0.9
>> rlist= 0.9
>> rvdw = 0.9
>>
>> tcoupl   = v-rescale
>> ref_t= 200
>> tau_t= 0.1
>> tc_grps  = System
>>
>> gen_vel  = yes
>> gen_temp = 300
>>
>> constraints  = all-bonds "
>>
>>
>> this is the error I found in the .log file:
>>
>> "Fatal error:
>> Too many LINCS warnings (1034)
>> If you know what you are doing you can adjust the lincs warning
>> threshold in your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem "
>>
>> I tired to comment the constrains part and all is working, but since
>> the
>> structure should not be altered too much, I think the constraints are
>> required (if I constrain only the h-bonds, it is also working).
>>
>> I've also added to the .mdp file the lines:
>> " lincs-order  = 4 (or 2 or 8)
>> lincs-iter   = 1 (or 2 or 10)
>> "
>> but it is still not working...
>>
>>
>> any of you have suggestions to solve the problem??
>> how is it possible to change the environment variable?
>>
>>
>> thanks in advance for your help
>> Emiliano
>>
>> --
>> Emiliano De Santis
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>

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Re: [gmx-users] LINCS warning during constrained md

[Mark Abraham]

Hi,

Those are all good things, but have you actually got out a molecular viewer
and looked at the input and output of your resolution conversion?

Mark

On Wed, Jul 12, 2017 at 4:25 PM edesantis  wrote:

> Hi,
> thanks for the prompt answer,
>
>
> I've found the same problem even if I try to convert the coarse grained
> pdb obtained from martinize.py, so in that case it should be not a
> problem to have the conversion, for this reason I though it is a
> methodological problem...
>
> I've seen the blowing-up issues , but I think:
> - the timestep is enough small  (0.0002)
> -the system should be enough minimized via the previous steps (in fact
> the sd converged to the machine precision in both cases, actually the
> potential energy is ~10^5, but I don't know how to reduce it, I tried a
> cg after the sd, but the proble is still there)
> -there in not any pressure coupling
> -I've tried a different temperature coupling (berensden, nose-hoover)
> and it doesn't work
> - the md stops at the first step, so there is not any .edr file produced
> to be looked at
>
>
>
> I don't know what else to do...
>
> maybe, do you know another conversion protocol to use??
>
>
> thank you again
> Emiliano
>
> On 2017-07-12 15:11, Mark Abraham wrote:
> > Hi,
> >
> > Sounds like you might be
> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
> > conversion doesn't work for your configuration. You should start by
> > doing a
> > visual check of the configuration for sanity, then follow the advice in
> > that link.
> >
> > Mark
> >
> > On Wed, Jul 12, 2017 at 3:04 PM edesantis 
> > wrote:
> >
> >> dear all,
> >>
> >> I am facing a problem with the conversion from Martini CG
> >> representation
> >> to All-atomistic one.
> >>
> >> I am using the initram.sh wrapper around the backward.py.
> >>
> >> There is a LINCS warning problem when the energy relaxation is
> >> performed
> >> using position restrained md
> >> (I've also tried to run grompp and mdrun commands directly from the
> >> terminal and the error persists, so it is not a wrapper problem).
> >>
> >> this is the .mdp file generated by the script:
> >>
> >> "define   = -DPOSRES
> >> integrator   = md
> >> nsteps   = 500
> >> dt   = 0.0002
> >> pbc  = xyz
> >>
> >> rcoulomb = 0.9
> >> rlist= 0.9
> >> rvdw = 0.9
> >>
> >> tcoupl   = v-rescale
> >> ref_t= 200
> >> tau_t= 0.1
> >> tc_grps  = System
> >>
> >> gen_vel  = yes
> >> gen_temp = 300
> >>
> >> constraints  = all-bonds "
> >>
> >>
> >> this is the error I found in the .log file:
> >>
> >> "Fatal error:
> >> Too many LINCS warnings (1034)
> >> If you know what you are doing you can adjust the lincs warning
> >> threshold in your mdp file
> >> or set the environment variable GMX_MAXCONSTRWARN to -1,
> >> but normally it is better to fix the problem "
> >>
> >> I tired to comment the constrains part and all is working, but since
> >> the
> >> structure should not be altered too much, I think the constraints are
> >> required (if I constrain only the h-bonds, it is also working).
> >>
> >> I've also added to the .mdp file the lines:
> >> " lincs-order  = 4 (or 2 or 8)
> >> lincs-iter   = 1 (or 2 or 10)
> >> "
> >> but it is still not working...
> >>
> >>
> >> any of you have suggestions to solve the problem??
> >> how is it possible to change the environment variable?
> >>
> >>
> >> thanks in advance for your help
> >> Emiliano
> >>
> >> --
> >> Emiliano De Santis
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
>
> --
> Emiliano De Santis
> --
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>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] LINCS warning during constrained md

[edesantis]

Hi,
thanks for the prompt answer,


I've found the same problem even if I try to convert the coarse grained 
pdb obtained from martinize.py, so in that case it should be not a 
problem to have the conversion, for this reason I though it is a 
methodological problem...


I've seen the blowing-up issues , but I think:
- the timestep is enough small  (0.0002)
-the system should be enough minimized via the previous steps (in fact 
the sd converged to the machine precision in both cases, actually the 
potential energy is ~10^5, but I don't know how to reduce it, I tried a 
cg after the sd, but the proble is still there)

-there in not any pressure coupling
-I've tried a different temperature coupling (berensden, nose-hoover) 
and it doesn't work
- the md stops at the first step, so there is not any .edr file produced 
to be looked at




I don't know what else to do...

maybe, do you know another conversion protocol to use??


thank you again
Emiliano

On 2017-07-12 15:11, Mark Abraham wrote:

Hi,

Sounds like you might be
http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
conversion doesn't work for your configuration. You should start by 
doing a

visual check of the configuration for sanity, then follow the advice in
that link.

Mark

On Wed, Jul 12, 2017 at 3:04 PM edesantis  
wrote:



dear all,

I am facing a problem with the conversion from Martini CG 
representation

to All-atomistic one.

I am using the initram.sh wrapper around the backward.py.

There is a LINCS warning problem when the energy relaxation is 
performed

using position restrained md
(I've also tried to run grompp and mdrun commands directly from the
terminal and the error persists, so it is not a wrapper problem).

this is the .mdp file generated by the script:

"define   = -DPOSRES
integrator   = md
nsteps   = 500
dt   = 0.0002
pbc  = xyz

rcoulomb = 0.9
rlist= 0.9
rvdw = 0.9

tcoupl   = v-rescale
ref_t= 200
tau_t= 0.1
tc_grps  = System

gen_vel  = yes
gen_temp = 300

constraints  = all-bonds "


this is the error I found in the .log file:

"Fatal error:
Too many LINCS warnings (1034)
If you know what you are doing you can adjust the lincs warning
threshold in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem "

I tired to comment the constrains part and all is working, but since 
the

structure should not be altered too much, I think the constraints are
required (if I constrain only the h-bonds, it is also working).

I've also added to the .mdp file the lines:
" lincs-order  = 4 (or 2 or 8)
lincs-iter   = 1 (or 2 or 10)
"
but it is still not working...


any of you have suggestions to solve the problem??
how is it possible to change the environment variable?


thanks in advance for your help
Emiliano

--
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Re: [gmx-users] LINCS warning during constrained md

[Mark Abraham]

Hi,

Sounds like you might be
http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
conversion doesn't work for your configuration. You should start by doing a
visual check of the configuration for sanity, then follow the advice in
that link.

Mark

On Wed, Jul 12, 2017 at 3:04 PM edesantis  wrote:

> dear all,
>
> I am facing a problem with the conversion from Martini CG representation
> to All-atomistic one.
>
> I am using the initram.sh wrapper around the backward.py.
>
> There is a LINCS warning problem when the energy relaxation is performed
> using position restrained md
> (I've also tried to run grompp and mdrun commands directly from the
> terminal and the error persists, so it is not a wrapper problem).
>
> this is the .mdp file generated by the script:
>
> "define   = -DPOSRES
> integrator   = md
> nsteps   = 500
> dt   = 0.0002
> pbc  = xyz
>
> rcoulomb = 0.9
> rlist= 0.9
> rvdw = 0.9
>
> tcoupl   = v-rescale
> ref_t= 200
> tau_t= 0.1
> tc_grps  = System
>
> gen_vel  = yes
> gen_temp = 300
>
> constraints  = all-bonds "
>
>
> this is the error I found in the .log file:
>
> "Fatal error:
> Too many LINCS warnings (1034)
> If you know what you are doing you can adjust the lincs warning
> threshold in your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem "
>
> I tired to comment the constrains part and all is working, but since the
> structure should not be altered too much, I think the constraints are
> required (if I constrain only the h-bonds, it is also working).
>
> I've also added to the .mdp file the lines:
> " lincs-order  = 4 (or 2 or 8)
> lincs-iter   = 1 (or 2 or 10)
> "
> but it is still not working...
>
>
> any of you have suggestions to solve the problem??
> how is it possible to change the environment variable?
>
>
> thanks in advance for your help
> Emiliano
>
> --
> Emiliano De Santis
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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[gmx-users] LINCS warning during constrained md

[edesantis]

dear all,

I am facing a problem with the conversion from Martini CG representation 
to All-atomistic one.


I am using the initram.sh wrapper around the backward.py.

There is a LINCS warning problem when the energy relaxation is performed 
using position restrained md
(I've also tried to run grompp and mdrun commands directly from the 
terminal and the error persists, so it is not a wrapper problem).


this is the .mdp file generated by the script:

"define   = -DPOSRES
integrator   = md
nsteps   = 500
dt   = 0.0002
pbc  = xyz

rcoulomb = 0.9
rlist= 0.9
rvdw = 0.9

tcoupl   = v-rescale
ref_t= 200
tau_t= 0.1
tc_grps  = System

gen_vel  = yes
gen_temp = 300

constraints  = all-bonds "


this is the error I found in the .log file:

"Fatal error:
Too many LINCS warnings (1034)
If you know what you are doing you can adjust the lincs warning 
threshold in your mdp file

or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem "

I tired to comment the constrains part and all is working, but since the 
structure should not be altered too much, I think the constraints are 
required (if I constrain only the h-bonds, it is also working).


I've also added to the .mdp file the lines:
" lincs-order  = 4 (or 2 or 8)
lincs-iter   = 1 (or 2 or 10)
"
but it is still not working...


any of you have suggestions to solve the problem??
how is it possible to change the environment variable?


thanks in advance for your help
Emiliano

--
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Re: [gmx-users] lincs warning

[Justin Lemkul]

On 3/14/17 2:57 AM, fatemeh ramezani wrote:

Dear gmx usersplease help me if you know how can I change lincs warning 
threshold in mdp file or in command?



The .mdp option is lincs-warnangle but you should not be toying with this option 
just to make errors go away; LINCS warnings indicate a severe physical problem 
in the system.  If you make the algorithm more permissive, you likely allow for 
nasty, unphysical distortion even if the run "finishes."


-Justin

--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] lincs warning

[fatemeh ramezani]

Dear gmx usersplease help me if you know how can I change lincs warning 
threshold in mdp file or in command?

thank you Fatemeh Ramezani
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Re: [gmx-users] LINCS warning

[Justin Lemkul]

On 8/25/16 5:56 AM, amitbe...@chemeng.iisc.ernet.in wrote:

Hello users,
I was trying to energy minimize my system of protein embedded in bilayer.
But I am receiving the following error:

Step -1, time -0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000942, max 0.149038 (between atoms 21616 and 21619)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=   50

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 11 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  2.3557852e+30
Maximum force =inf on atom 34347
Norm of force =inf

what approach should I use to get rid of this problem?



Infinite force most likely means you have atoms on top of each other.  mdrun 
tells you where the (first) problem is - atom 34347.  Inspect that area visually 
and figure out what part of your system preparation went wrong.


-Justin

--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] LINCS warning

[amitbehra]

Hello users,
I was trying to energy minimize my system of protein embedded in bilayer.
But I am receiving the following error:

Step -1, time -0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000942, max 0.149038 (between atoms 21616 and 21619)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=   50

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 11 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  2.3557852e+30
Maximum force =inf on atom 34347
Norm of force =inf

what approach should I use to get rid of this problem?

Regards,
Amit Behera


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Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

[Tsjerk Wassenaar]

Hi Antara,

What commands did you use? At least make sure you add -rdd 1.6 to the
command line of mdrun, because the default value is too small for coarse
grain simulations.

Cheers,

Tsjerk

On Fri, May 13, 2016 at 8:12 PM, Antara mazumdar 
wrote:

> Dear users,
>
> I am trying to run a coarse grained simulation of a membrane protein in a
> mixed lipid billayer using martini model 2.2. I have already performed all
> the equilibration steps successfully on my desktop with GROMACS 5.1.0.
> However, when i try to execute its production run in parallel(having
> gromacs 5.1 version installed)  it complains of LINCS warning and
> terminates at step 0. But on the contrary, it runs on the desktop
> successfully. Kindly suggest something and please let me know if any more
> information is required from my side.
>
>
> Thanks!!
>
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
>
>
>
> On Fri, May 13, 2016 at 11:11 PM, Antara mazumdar  >
> wrote:
>
> > Dear gromacs users,
> >
> > I am trying to run a coarse grained simulation of a membrane protein in a
> > mixed lipid billayer using martini model. I have already performed all
> the
> > equilibration steps successfully on my desktop. However, when i try to
> > execute its production run in parallel it complains of LINCS warning and
> > terminates at step 0. But on the contrary, it runs on the desktop
> > successfully. Kindly suggest something and please let me know if any more
> > information is required from my side.
> >
> >
> > Thanks!!
> >
> >
> >
> > Kind Regards,
> > Antara
> >
> > --
> > Junior research fellow(project)
> > Systems biology group
> > CSIR-Institute of Genomics & Integrative Biology
> > South Campus
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> > --
> >
> >
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Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

[Antara mazumdar]

Dear users,

I am trying to run a coarse grained simulation of a membrane protein in a
mixed lipid billayer using martini model 2.2. I have already performed all
the equilibration steps successfully on my desktop with GROMACS 5.1.0.
However, when i try to execute its production run in parallel(having
gromacs 5.1 version installed)  it complains of LINCS warning and
terminates at step 0. But on the contrary, it runs on the desktop
successfully. Kindly suggest something and please let me know if any more
information is required from my side.


Thanks!!

Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--



On Fri, May 13, 2016 at 11:11 PM, Antara mazumdar 
wrote:

> Dear gromacs users,
>
> I am trying to run a coarse grained simulation of a membrane protein in a
> mixed lipid billayer using martini model. I have already performed all the
> equilibration steps successfully on my desktop. However, when i try to
> execute its production run in parallel it complains of LINCS warning and
> terminates at step 0. But on the contrary, it runs on the desktop
> successfully. Kindly suggest something and please let me know if any more
> information is required from my side.
>
>
> Thanks!!
>
>
>
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
>
>
>
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Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

[Mark Abraham]

Hi,

Several things will make it easier to help - particularly your GROMACS
versions and how you ran mdrun. See also http://www.gromacs.org/Support

Mark

On Fri, May 13, 2016 at 7:42 PM Antara mazumdar 
wrote:

> Dear gromacs users,
>
> I am trying to run a coarse grained simulation of a membrane protein in a
> mixed lipid billayer using martini model. I have already performed all the
> equilibration steps successfully on my desktop. However, when i try to
> execute its production run in parallel it complains of LINCS warning and
> terminates at step 0. But on the contrary, it runs on the desktop
> successfully. Kindly suggest something and please let me know if any more
> information is required from my side.
>
>
> Thanks!!
>
>
>
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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[gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

[Antara mazumdar]

Dear gromacs users,

I am trying to run a coarse grained simulation of a membrane protein in a
mixed lipid billayer using martini model. I have already performed all the
equilibration steps successfully on my desktop. However, when i try to
execute its production run in parallel it complains of LINCS warning and
terminates at step 0. But on the contrary, it runs on the desktop
successfully. Kindly suggest something and please let me know if any more
information is required from my side.


Thanks!!



Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--
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[gmx-users] LINCS warning of QMMM simulation

[andrian]

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus 
protonated water... my simulation was going well until LINCS warning 
appeared.


"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation 
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds 
that rotated more than 30 degrees"


i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol.itp"
#endif

#include "waterH.acpype/waterH_GMX.itp"

; Include Position restraint file
#ifdef POSRES_WATER
#include "posre_water.itp"
#endif

[ system ]
 alkohol

[ molecules ]
; Compoundnmols
alkohol   1
waterH  1


*
here is my alkohol itp file

; alkohol_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ atomtypes ]
;name   bond_type at.nummass charge   ptype   sigma 
epsilon   Amb
 c3   c3  60.0  0.0   A 3.39967e-01 4.57730e-01 
; 1.91  0.1094
 h1   h1  10.0  0.0   A 2.47135e-01 6.56888e-02 
; 1.39  0.0157
 oh   oh  80.0  0.0   A 3.06647e-01 8.80314e-01 
; 1.72  0.2104
 cl   cl 170.0  0.0   A 3.47094e-01 1.10876e+00 
; 1.95  0.2650
 hc   hc  10.0  0.0   A 2.64953e-01 6.56888e-02 
; 1.49  0.0157
 ho   ho  10.0  0.0   A 0.0e+00 0.0e+00 
; 0.00  0.

 LA  LA  10.0  0.0   A 0.00+00 0.0e+00

[ moleculetype ]
;namenrexcl
 alkohol  3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot   
bond_type

 1   c3 1   UNL C1 0.122400 12.01000 ; qtot 0.122
 2   c3 1   UNLC12 0.015700 12.01000 ; qtot 0.138
 3   h1 1   UNL H3 0.058200  1.00800 ; qtot 0.196
 4   oh 1   UNL O4-0.593801 16.0 ; qtot -0.398
 5   h1 1   UNLH15 0.058200  1.00800 ; qtot -0.339
 6   c3 1   UNLC26-0.083400 12.01000 ; qtot -0.423
 7   h1 1   UNLH27 0.086700  1.00800 ; qtot -0.336
 8   cl 1   UNLCL8-0.208400 35.45000 ; qtot -0.544
 9   c3 1   UNLC39-0.097100 12.01000 ; qtot -0.642
10   hc 1   UNLH3   10 0.053700  1.00800 ; qtot -0.588
11   hc 

[gmx-users] LINCS WARNING

[masoud keramati]

Hi to all dear gmx users

during the Energy Minimization i got this warning in first few steps
after step 20
"step 20: Water molecule starting at atom 34209 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate."

but after 3021 steps it was converged to Fmax < 1000.

then i start the Equilibration and in the zero to 4 steps i got this:
"Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018591, max 0.374857 (between atoms 2409 and 2411)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length"

in the step 5i got this and mdrun was terminate.
" Water molecule starting at atom 32146 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

WARNING: Listed nonbonded interaction between particles 2312 and 2326
at distance 4211.247 which is larger than the table limit 2.034 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.


Segmentation fault (core dumped)"

my Equilibration is:

define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 500   ; save coordinates every 1.0 ps
nstvout = 500   ; save velocities every 1.0 ps
nstenergy   = 500   ; save energies every 1.0 ps
nstlog  = 500   ; update log file every 1.0 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm= lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.0   ; short-range electrostatic cutoff (in 
nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in 
nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.135 ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = nose-hoover   ; modified Berendsen thermostat
tc-grps = system; two coupling groups - more accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one for each 
group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed



tnx for your help
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Re: [gmx-users] LINCS WARNING

[Justin Lemkul]

On 10/6/15 3:26 AM, Vy Phan wrote:

Dear all gromacs Users!
I want to run a simulation with the system protein-ligand (I have several
ligands).
With EM, nvt, npt step I put position restraint for the ligands and all
thing was fine. After that, I run production simulation without position
restraint of ligands. I saw the ligand move out of the initial position and
simulation was stopped.

Did the LINCS warning  happen because this system is not stable ?


Yes.


How can I keep the continuous running simulation without the  LINCS
warnings? I want  the ligands are free to move and find their binding sites.



Either your ligand topology is not stable or your run settings are not sensible. 
 Please see any of the million or so posts in the gmx-users mailing list 
archive regarding similar or identical situations.


-Justin


This is the warnings:
Too many LINCS warnings (1000)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

Thank you so much for any suggestions
Tuong Vy



--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] LINCS WARNING

[Vy Phan]

Dear all gromacs Users!
I want to run a simulation with the system protein-ligand (I have several
ligands).
With EM, nvt, npt step I put position restraint for the ligands and all
thing was fine. After that, I run production simulation without position
restraint of ligands. I saw the ligand move out of the initial position and
simulation was stopped.

Did the LINCS warning  happen because this system is not stable ?
How can I keep the continuous running simulation without the  LINCS
warnings? I want  the ligands are free to move and find their binding sites.

This is the warnings:
Too many LINCS warnings (1000)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

Thank you so much for any suggestions
Tuong Vy
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Re: [gmx-users] LINCS WARNING

[Vy Phan]

Dear Justin,
I am so thankful for you kindly reply. Now, I can solve this problem.

Tuong Vy

On Tue, Oct 6, 2015 at 11:49 PM, Justin Lemkul  wrote:

>
>
> On 10/6/15 3:26 AM, Vy Phan wrote:
>
>> Dear all gromacs Users!
>> I want to run a simulation with the system protein-ligand (I have several
>> ligands).
>> With EM, nvt, npt step I put position restraint for the ligands and all
>> thing was fine. After that, I run production simulation without position
>> restraint of ligands. I saw the ligand move out of the initial position
>> and
>> simulation was stopped.
>>
>> Did the LINCS warning  happen because this system is not stable ?
>>
>
> Yes.
>
> How can I keep the continuous running simulation without the  LINCS
>> warnings? I want  the ligands are free to move and find their binding
>> sites.
>>
>>
> Either your ligand topology is not stable or your run settings are not
> sensible.  Please see any of the million or so posts in the gmx-users
> mailing list archive regarding similar or identical situations.
>
> -Justin
>
> This is the warnings:
>> Too many LINCS warnings (1000)
>> If you know what you are doing you can adjust the lincs warning threshold
>> in your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem
>>
>> Thank you so much for any suggestions
>> Tuong Vy
>>
>>
> --
> ==
>
> 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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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>
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[gmx-users] LINCS WARNING

[Sun Iba]

Hello Everyone
I am simulation a protein as per the lysozyme tutorial. MY simulation got
dumped at final mdrun step. It is showing following warning :

Command line:
  gmx mdrun -deffnm md_0_1

Reading file md_0_1.tpr, VERSION 5.0.5 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads
starting mdrun 'AMYLOID BETA A4 PROTEIN'
50 steps,   2500.0 ps.

Step 166, time 0.83 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000162, max 0.000714 (between atoms 158 and 159)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
628629   30.00.1090   0.1090  0.1090

Step 170, time 0.85 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000234, max 0.005085 (between atoms 623 and 624)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
623624   73.10.1090   0.1084  0.1090
628629   55.10.1090   0.1089  0.1090

Step 171, time 0.855 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.023399, max 1.013176 (between atoms 623 and 624)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
623624   89.90.1084   0.2194  0.1090
Wrote pdb files with previous and current coordinates

Step 172, time 0.86 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000453, max 0.015917 (between atoms 628 and 629)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
623624   44.80.2194   0.1084  0.1090
628629   75.50.1093   0.1073  0.1090

Step 173, time 0.865 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.639970, max 23.410875 (between atoms 628 and 629)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
619621   30.30.1339   0.1284  0.1335
621622   46.90.1013   0.1019  0.1010
623624   89.70.1084   1.7118  0.1090
623625   72.50.1530   0.2719  0.1529
623638   43.10.1525   0.1587  0.1522
625626   46.90.1091   0.1372  0.1090
625627   61.50.1093   0.1643  0.1090
625628   89.30.1530   0.3458  0.1529
628629   90.00.1073   2.6608  0.1090
628630   74.10.1531   0.2413  0.1529
628634   88.30.1530   0.2401  0.1529
634635   41.20.1091   0.1433  0.1090
634636   38.20.1091   0.1357  0.1090
634637   39.00.1091   0.1380  0.1090
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 623 and 629
at distance 2.823 which is larger than the table limit 2.042 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.



Step 174, time 0.87 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2.212190, max 85.046806 (between atoms 623 and 624)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
260263   90.00.1090   0.3693  0.1090
621622   70.20.1019   0.1815  0.1010
621623   41.50.1556   0.2046  0.1449
623624   90.51.7119   9.3791  0.1090
623625  126.50.2719   0.4357  0.1529
623638   62.10.1587   0.1499  0.1522
625626   96.20.1372   3.6085  0.1090
625627  115.30.1643   0.8026  0.1090
625628  115.40.3458   1.3529  0.1529
628630  125.40.2413   0.8808  0.1529
628634  147.00.2401   0.6961  0.1529
630633  134.30.0801   0.0868  0.1090
634635  118.30.1433   0.3006  0.1090
634636   77.60.1357   0.2433  0.1090
634637   56.30.1380   0.1960  0.1090
638640   33.70.1388   0.0773  0.1335
Wrote pdb files with previous and current coordinates

Step 175, time 0.875 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 14884.476208, max 642183.562500 (between atoms 634 and 636)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
227229   30.30.1090   0.1118  0.1090
234236   90.00.1090   1.5776  0.1090
249250   89.90.1090   0.4785  0.1090

Re: [gmx-users] LINCS WARNING

[Justin Lemkul]

On 7/14/15 3:07 AM, Sun Iba wrote:

Hello Everyone
I am simulation a protein as per the lysozyme tutorial. MY simulation got
dumped at final mdrun step. It is showing following warning :

Command line:
   gmx mdrun -deffnm md_0_1

Reading file md_0_1.tpr, VERSION 5.0.5 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads
starting mdrun 'AMYLOID BETA A4 PROTEIN'
50 steps,   2500.0 ps.

Step 166, time 0.83 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000162, max 0.000714 (between atoms 158 and 159)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 628629   30.00.1090   0.1090  0.1090

Step 170, time 0.85 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000234, max 0.005085 (between atoms 623 and 624)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 623624   73.10.1090   0.1084  0.1090
 628629   55.10.1090   0.1089  0.1090

Step 171, time 0.855 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.023399, max 1.013176 (between atoms 623 and 624)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 623624   89.90.1084   0.2194  0.1090
Wrote pdb files with previous and current coordinates

Step 172, time 0.86 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000453, max 0.015917 (between atoms 628 and 629)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 623624   44.80.2194   0.1084  0.1090
 628629   75.50.1093   0.1073  0.1090

Step 173, time 0.865 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.639970, max 23.410875 (between atoms 628 and 629)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 619621   30.30.1339   0.1284  0.1335
 621622   46.90.1013   0.1019  0.1010
 623624   89.70.1084   1.7118  0.1090
 623625   72.50.1530   0.2719  0.1529
 623638   43.10.1525   0.1587  0.1522
 625626   46.90.1091   0.1372  0.1090
 625627   61.50.1093   0.1643  0.1090
 625628   89.30.1530   0.3458  0.1529
 628629   90.00.1073   2.6608  0.1090
 628630   74.10.1531   0.2413  0.1529
 628634   88.30.1530   0.2401  0.1529
 634635   41.20.1091   0.1433  0.1090
 634636   38.20.1091   0.1357  0.1090
 634637   39.00.1091   0.1380  0.1090
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 623 and 629
at distance 2.823 which is larger than the table limit 2.042 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.



Step 174, time 0.87 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2.212190, max 85.046806 (between atoms 623 and 624)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 260263   90.00.1090   0.3693  0.1090
 621622   70.20.1019   0.1815  0.1010
 621623   41.50.1556   0.2046  0.1449
 623624   90.51.7119   9.3791  0.1090
 623625  126.50.2719   0.4357  0.1529
 623638   62.10.1587   0.1499  0.1522
 625626   96.20.1372   3.6085  0.1090
 625627  115.30.1643   0.8026  0.1090
 625628  115.40.3458   1.3529  0.1529
 628630  125.40.2413   0.8808  0.1529
 628634  147.00.2401   0.6961  0.1529
 630633  134.30.0801   0.0868  0.1090
 634635  118.30.1433   0.3006  0.1090
 634636   77.60.1357   0.2433  0.1090
 634637   56.30.1380   0.1960  0.1090
 638640   33.70.1388   0.0773  0.1335
Wrote pdb files with previous and current coordinates

Step 175, time 0.875 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 14884.476208, max 642183.562500 (between atoms 634 and 636)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 227229   30.30.1090   0.1118  0.1090
 234236   90.0

Re: [gmx-users] LINCS warning

[Justin Lemkul]

On 4/28/14, 1:37 AM, Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU) wrote:

Dear Gromacs user,

After I give the command for nvt, I get the following error:
starting mdrun 'Protein in water'
15 steps,300.0 ps.

Step 0, time 0 (ps)  LINCS WARNING


If the run crashes at step zero, it suggests a catastrophic failure, i.e. the 
input configuration is not stable enough to simulate or there is a topology problem.



relative constraint deviation after LINCS:
rms 0.410417, max 7.601056 (between atoms 188 and 192)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 177179   40.70.1342   0.2195  0.1330
 179181   69.60.1484   0.2977  0.1470
 179180   51.10.1005   0.1744  0.1000
 181195   75.80.1543   0.2575  0.1530
 181182   77.00.1549   0.6596  0.1530
 182183   47.80.1549   0.3570  0.1530
 183186   76.80.1407   1.1049  0.1390
 183184   76.10.1406   0.9974  0.1390
 186187   69.80.1097   0.3696  0.1090
 188192   79.10.1403   1.1955  0.1390
 188189   72.00.1099   0.3759  0.1090
 190192   77.90.1404   1.1212  0.1390
 190191   71.50.1099   0.3818  0.1090
 195197   34.80.1345   0.1997  0.1330
 195196   39.90.1237   0.1807  0.1230
4571   4569   40.00.1404   0.0953  0.1400
4570   4569   91.20.1245   0.1846  0.1230
4572   4571   31.30.1005   0.1253  0.1000
 184188   41.10.1397   0.2396  0.1390
 184185   72.10.1097   0.4012  0.1090
 193194   82.90.1015   0.6012  0.1000
Wrote pdb files with previous and current coordinates
step 0
Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2524.656192, max 85802.020979 (between atoms 170 and 177)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 170177   81.90.1793 13127.8622  0.1530
 177179   94.90.2195 12873.2695  0.1330
 179181   88.60.2977 4411.0838  0.1470
 181195   96.60.2575 963.1998  0.1530
 195197   87.40.1997 250.2422  0.1330
 195196   80.60.1807 246.3256  0.1230
 181182   83.50.6596 33817.6412  0.1530
 182183   90.90.3570 1629245.5886  0.1530
 179180  150.70.1744 806.4780  0.1000
 177178   86.50.1487 13025.8466  0.1230
 170171  123.70.1636 1099.0521  0.1530
 172174  112.90.1334 124.2084  0.1330
 172173  119.80.1234 122.9154  0.1230
 174176   41.30.1000  19.2568  0.1000
 141149   30.50.1530   0.1924  0.1530
 149151  125.20.1330  18.9674  0.1330
 149150   34.10.1230   0.1614  0.1230
 151153   35.80.1471  28.7745  0.1470
 151152   83.30.1000  18.9746  0.1000
 166167  115.50.1238 341.2685  0.1230
 153166  117.80.1538 365.5008  0.1530
 153154   37.00.1531  14.8979  0.1530
 154155   90.80.1530  15.6791  0.1530
 155158   33.40.1390   0.1782  0.1390
 155156   32.80.1390   0.1771  0.1390
 168170  141.40.1596 1274.6369  0.1470
 168169   93.70.1015 232.5375  0.1000

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 12958124.333813, max 292691795.227618 (between atoms 184 and 188)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 203204   32.10.1470   0.1744  0.1470
 201202   74.00.1532   1.1957  0.1530
 202203  117.70.1530   0.3991  0.1530
 208210   59.20.1359   3.5580  0.1330
 208209   73.20.1256   1.9933  0.1230
 210212   74.80.1480   1.9178  0.1470
 210211   93.80.1007   1.5815  0.1000
 177179   94.90.2195 12873.2691  0.1330
 177178   86.50.1487 13025.8467  0.1230
 170177   81.90.1793 13127.8623  0.1530
 170171  123.70.1636 1099.0521  0.1530
 172174  112.90.1334 124.2084  0.1330
 174176   41.30.1000  19.2568  0.1000
 172173  119.80.1234 122.9154  0.1230
 168170  141.40.1596 1274.6369  0.1470
 168169   93.70.1015 232.5375  0.1000
 166167  115.50.1238 341.2681  0.1230
 153166  117.80.1538 365.5039  0.1530
 153154   37.00.1531  14.8978  0.1530
 151153   35.80.1471  28.7776  0.1470
 179181   88.60.2977 4411.0814  0.1470
 179180  150.70.1744 806.4798  0.1000
 

[gmx-users] LINCS warning

[Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU)]

Dear Gromacs user,

After I give the command for nvt, I get the following error:
starting mdrun 'Protein in water'
15 steps,300.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.410417, max 7.601056 (between atoms 188 and 192)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
177179   40.70.1342   0.2195  0.1330
179181   69.60.1484   0.2977  0.1470
179180   51.10.1005   0.1744  0.1000
181195   75.80.1543   0.2575  0.1530
181182   77.00.1549   0.6596  0.1530
182183   47.80.1549   0.3570  0.1530
183186   76.80.1407   1.1049  0.1390
183184   76.10.1406   0.9974  0.1390
186187   69.80.1097   0.3696  0.1090
188192   79.10.1403   1.1955  0.1390
188189   72.00.1099   0.3759  0.1090
190192   77.90.1404   1.1212  0.1390
190191   71.50.1099   0.3818  0.1090
195197   34.80.1345   0.1997  0.1330
195196   39.90.1237   0.1807  0.1230
   4571   4569   40.00.1404   0.0953  0.1400
   4570   4569   91.20.1245   0.1846  0.1230
   4572   4571   31.30.1005   0.1253  0.1000
184188   41.10.1397   0.2396  0.1390
184185   72.10.1097   0.4012  0.1090
193194   82.90.1015   0.6012  0.1000
Wrote pdb files with previous and current coordinates
step 0
Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2524.656192, max 85802.020979 (between atoms 170 and 177)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
170177   81.90.1793 13127.8622  0.1530
177179   94.90.2195 12873.2695  0.1330
179181   88.60.2977 4411.0838  0.1470
181195   96.60.2575 963.1998  0.1530
195197   87.40.1997 250.2422  0.1330
195196   80.60.1807 246.3256  0.1230
181182   83.50.6596 33817.6412  0.1530
182183   90.90.3570 1629245.5886  0.1530
179180  150.70.1744 806.4780  0.1000
177178   86.50.1487 13025.8466  0.1230
170171  123.70.1636 1099.0521  0.1530
172174  112.90.1334 124.2084  0.1330
172173  119.80.1234 122.9154  0.1230
174176   41.30.1000  19.2568  0.1000
141149   30.50.1530   0.1924  0.1530
149151  125.20.1330  18.9674  0.1330
149150   34.10.1230   0.1614  0.1230
151153   35.80.1471  28.7745  0.1470
151152   83.30.1000  18.9746  0.1000
166167  115.50.1238 341.2685  0.1230
153166  117.80.1538 365.5008  0.1530
153154   37.00.1531  14.8979  0.1530
154155   90.80.1530  15.6791  0.1530
155158   33.40.1390   0.1782  0.1390
155156   32.80.1390   0.1771  0.1390
168170  141.40.1596 1274.6369  0.1470
168169   93.70.1015 232.5375  0.1000

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 12958124.333813, max 292691795.227618 (between atoms 184 and 188)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
203204   32.10.1470   0.1744  0.1470
201202   74.00.1532   1.1957  0.1530
202203  117.70.1530   0.3991  0.1530
208210   59.20.1359   3.5580  0.1330
208209   73.20.1256   1.9933  0.1230
210212   74.80.1480   1.9178  0.1470
210211   93.80.1007   1.5815  0.1000
177179   94.90.2195 12873.2691  0.1330
177178   86.50.1487 13025.8467  0.1230
170177   81.90.1793 13127.8623  0.1530
170171  123.70.1636 1099.0521  0.1530
172174  112.90.1334 124.2084  0.1330
174176   41.30.1000  19.2568  0.1000
172173  119.80.1234 122.9154  0.1230
168170  141.40.1596 1274.6369  0.1470
168169   93.70.1015 232.5375  0.1000
166167  115.50.1238 341.2681  0.1230
153166  117.80.1538 365.5039  0.1530
153154   37.00.1531  14.8978  0.1530
151153   35.80.1471  28.7776  0.1470
179181   88.60.2977 4411.0814  0.1470
179180  150.70.1744 806.4798  0.1000
212217  118.10.1531   1.2961  0.1530
212213  109.40.1531   1.3254  0.1530
213214   39.00.1530   0.2085  0.1530
155156   32.80.1390   0.1771  0.1390
155158   33.40.1390   0.1782  0.1390
154155   90.80.1530  15.6794  0.1530
151