[gmx-users] Re: Help - LINCS WARNING: bonds that rotated more than 30 degrees
Justin A. Lemkul
jalemkul at vt.edu
Mon Dec 6 13:31:08 CET 2010
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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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