[gmx-users] Re: Help - LINCS WARNING: bonds that rotated more than 30 degrees

Mon, 06 Dec 2010 04:34:29 -0800
Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private help service. I am CC'ing the list and would ask that anything further be posted there. 


Before posting anything to the list, check the list archive.  Your problem has 
been posted and answered literally thousands of times.  Even better, the Gromacs 
site is full of helpful information, like the following:


http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

YUVRAJ UBOVEJA wrote:

Hello Sir

Good Morning


I am working on 1CRL.pdb (lipase with open lid). It had NAG which was 
removed from the pdb.
I am using gromacs 4.5.3. I am posting all my steps here and all 
necessary .mdp files are attached.


1. pdb2gmx  (forcefield used amber99sb-ildn with tip3p model)

 
2) editconf -bt dodecahedron -f 1.gro -c -d 1.0


3) genbox -cp 1CRL_step2.pdb -cs tip4p.gro -o 1CRL_b4em.pdb -p topol.top

4) grompp -f em.mdp -c 1CRL_b4em.pdb -p 1CRL_top1.top -o 1CRL_em.tpr


5) genion -p -s 1CRL_em.tpr -o 1CRL_ion.pdb -pname NA+ -np 17 -g 
1CRL_ion.log     

6) grompp -f em.mdp -c 1CRL_ion.pdb -p topol.top -o 1CRL_em.tpr    


7) mdrun -s 1CRL_em.tpr -o 1CRL_em.trr -c 1CRL_b4pr.pdb -g em.log -e em.edr


8) grompp -f pr.mdp -c 1CRL_b4pr.pdb -r 1CRL_b4pr.pdb -p topol.top -o 
1CRL_pr.tpr


9) mdrun -s 1CRL_pr.tpr -o 1CRL_pr.trr -c 1CRL_b4md.pdb -g pr.log -e pr.edr

It is giving Error as follows:
*
Step 7, time 0.014 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000039, max 0.000512 (between atoms 5125 and 5126)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5126   31.8    0.1010   0.1009      0.1010

Step 8, time 0.016 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000018, max 0.000869 (between atoms 5125 and 5126)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5126   33.9    0.1009   0.1011      0.1010

Step 32, time 0.064 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000035, max 0.001516 (between atoms 5125 and 5127)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5127   34.2    0.1010   0.1008      0.1010

Step 33, time 0.066 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000041, max 0.001609 (between atoms 5125 and 5126)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5127   32.7    0.1008   0.1009      0.1010

Step 39, time 0.078 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000038, max 0.001576 (between atoms 5125 and 5126)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5127   34.5    0.1010   0.1011      0.1010

Step 40, time 0.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000049, max 0.002593 (between atoms 5125 and 5127)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5127   34.3    0.1011   0.1013      0.1010

Step 41, time 0.082 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000025, max 0.000573 (between atoms 5125 and 5127)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5127   31.5    0.1013   0.1011      0.1010

Step 42, time 0.084 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000037, max 0.001815 (between atoms 5125 and 5127)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5127   34.7    0.1011   0.1008      0.1010

Step 43, time 0.086 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000033, max 0.001302 (between atoms 5125 and 5127)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5127   32.2    0.1008   0.1009      0.1010

Step 51, time 0.102 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000036, max 0.001418 (between atoms 5125 and 5127)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5126   30.5    0.1012   0.1010      0.1010

Step 55, time 0.11 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000048, max 0.002660 (between atoms 4571 and 4573)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4571   4572   36.5    0.1010   0.1010      0.1010

Step 56, time 0.112 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000042, max 0.002092 (between atoms 4571 and 4573)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4571   4572   36.4    0.1010   0.1010      0.1010

Step 57, time 0.114 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000028, max 0.000763 (between atoms 4571 and 4573)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4571   4572   31.8    0.1010   0.1010      0.1010

Step 63, time 0.126 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000027, max 0.000427 (between atoms 4571 and 4572)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4571   4573   32.7    0.1011   0.1010      0.1010

Step 64, time 0.128 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000068, max 0.003175 (between atoms 5125 and 5126)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 64, time 0.128 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000040, max 0.001591 (between atoms 4571 and 4573)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5127   35.2    0.1010   0.1012      0.1010
   4571   4573   37.2    0.1010   0.1008      0.1010

Step 65, time 0.13 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000049, max 0.002173 (between atoms 5125 and 5126)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 65, time 0.13 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000027, max 0.000553 (between atoms 4571 and 4573)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5127   35.0    0.1012   0.1011      0.1010
   4571   4573   31.0    0.1008   0.1009      0.1010

Step 66, time 0.132 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000038, max 0.001188 (between atoms 5125 and 5127)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5127   35.6    0.1011   0.1009      0.1010

Step 67, time 0.134 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000050, max 0.002202 (between atoms 5125 and 5126)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5127   31.4    0.1009   0.1009      0.1010

Step 71, time 0.142 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000041, max 0.001740 (between atoms 5125 and 5126)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5126   34.6    0.1010   0.1012      0.1010

Step 72, time 0.144 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000033, max 0.000836 (between atoms 5125 and 5127)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5126   34.2    0.1012   0.1011      0.1010

Step 73, time 0.146 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000040, max 0.001326 (between atoms 5125 and 5126)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5126   38.5    0.1011   0.1009      0.1010

Step 74, time 0.148 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000028, max 0.000900 (between atoms 5125 and 5127)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5126   32.6    0.1009   0.1010      0.1010
^C

Received the INT signal, stopping at the next NS step


Step 80, time 0.16 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000039, max 0.001703 (between atoms 5125 and 5126)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5126   30.8    0.1010   0.1012      0.1010

Step 81, time 0.162 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000045, max 0.002178 (between atoms 5125 and 5126)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5125   5126   30.8    0.1012   0.1012      0.101*0


Kindly give me a solution.

Thanks


Yuvraj Uboveja
M. Tech Bioinformatics
CCNSB, IIIT-H



On Thu, Nov 18, 2010 at 5:25 PM, Justin A. Lemkul <jalem...@vt.edu 
<mailto:jalem...@vt.edu>> wrote:




    YUVRAJ UBOVEJA wrote:

        Dear Dr. Lemkul

        I was following your tutorial on lysozyme in water. In which you
        have suggested to remove crystal water from the PDB file. As I
        am an amateur in simulations, just started with GROMACS
        Please find some time to answer my queries which could be very
        silly in nature.

        Why do we want to delete crystal water?


    I did this for ease of understanding.  In previous Gromacs versions,
    crystal waters and those added later showed up as separate "SOL"
    blocks in the topology, which was not always easy to understand.


        How do we come to know whether crystal water is required for our
        simulation or not.


    If these water molecules serve a functional role, do not remove
    them.  The paper that discusses the structure should have this
    information.  Most of the time, crystal waters are unimportant.


        What is difference between crystal water already present in PDB
        and water moleclues we add in solvation step. Is there any
        functional difference wrt to simulation.


    A crystal water comes from solvent conditions used during x-ray
    diffraction. Anything else is added.  Functional roles are
    determined experimentally (see above comment).


        One more thing how do we decide whether to use OPLS / AMBER
        force field for our system (in my case it is lipase 1TRH). I got
        to know that OPLS parameter have been created taking explicitly
        solvent molecule in consideration. So in my view OPLS is more
        better for solvating a protein for any solvent simulations.


    I don't know how you came to this conclusions.  Any of the force
    fields provided in Gromacs are quite suitable to protein
    simulations.  They are all based on different quantum mechanical or
    thermodynamic assumptions.  You should spend some (significant) time
    reading about each of the force fields and what they assume, and any
    limitations they might have.

    -Justin


        Thanks in anticipation.

        Best Regards



    -- 
    ========================================


    Justin A. Lemkul
    Ph.D. Candidate
    ICTAS Doctoral Scholar
    MILES-IGERT Trainee
    Department of Biochemistry
    Virginia Tech
    Blacksburg, VA
    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

    ========================================




--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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