[gmx-users] LINCS warning in md run

[reisingere at rostlab.informatik.tu-muenchen.de]

I need the rest of the structure just as it is now because I want to do
electrostatic analysis with it.
I just added the phosphate manually and so I want to minimize and run a
short MD with it.

I added the dihedraltype of the amber database
(http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p)
to the ffbonded file.
And additionally I looked at the protein and made all the residues which
could somehow influence the protein flexible so that eventual clashes can
be repaired.
But still I got the error:

..Step 3612, time 3.612 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000008, max 0.000031 (between atoms 975 and 978)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    976    979   32.6    0.0961   0.0960      0.0960

Step 3613, time 3.613 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000237, max 0.001400 (between atoms 976 and 979)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    976    979   33.4    0.0960   0.0959      0.0960
..

Too many LINCS warnings (1000)


I already minimized the protein and everything was fine. There were no
errors:

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -7.7436938e+05
Maximum force     =  8.6871973e+03 on atom 979
Norm of force     =  7.1224258e+01

gcq#49: "You Could Make More Money As a Butcher" (F. Zappa)


Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -7.7436938e+05
Maximum force     =  8.6871973e+03 on atom 979
Norm of force     =  7.1224258e+01


And also during the grompp run there are no errors.
Can you please help me to find out where the problem lies?


Thank you,
 Eva


>
>
> On 9/13/12 5:50 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Ah okey. Thank you.
>> I will write them.
>>
>> Hmm, but the protein is a crystal structure from pdb with a resolution
>> of
>> 1.2. I already added the hydrogen atoms to this structure and there I
>> already minimized them and made a md run. And there were no errors. And
>> now I only added the phosphate to the minimized structure. So I thought
>> that I only had to minimize the phosphate and the residue it bound on.
>> Or is there a mistake in my thought here?
>
> If adding the phosphate resulted in a crash, then clearly that's the
> problem.  I
> don't understand why you would run EM on just the phosphate and keep the
> rest of
> the protein structure frozen.  Again, that potentially prevents clashes
> from
> being resolved.  I don't understand what value there is in only minimizing
> the
> phosphate.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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