[gmx-users] Unstable Minimizations

[Justin A. Lemkul]

On 1/10/10 5:18 PM, Jack Shultz wrote:
> I am trying to get this workflow opperational. However, my systems are
> getting unstable. I have preped two mdp files: 1) one for restrained 2)
> unrestrained. LINCS errors appear for restrained and unrestrained has
> infinite energy appearing.
> http://boinc.drugdiscoveryathome.com/_em_restrained_rcs_mdrun.txt_
> <http://boinc.drugdiscoveryathome.com/em_restrained_rcs_mdrun.txt>
> __

This log file shows several "long bond" warnings, which may be the root of your 
problem.  See here:

http://www.gromacs.org/Documentation/Errors#Long_bonds_and.2for_missing_atoms

Since your minimization is failing immediately, there is something physically 
unreasonable about your structure, such that EM cannot resolve the problem. 
Note, too, that one of the long bond warnings pertained to atom 1668, which is 
the location of the first LINCS warning.  Coincidence?  Not likely.  Re-examine 
the starting structure and figure out if anything is missing or poorly 
reconstructed (e.g., from initially missing atoms).

> This is where I get the LINCS Warnings
> Step -1, time -0.001 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.461520, max 14.428611 (between atoms 1668 and 1669)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+04
>     Number of steps    =          100
> Warning: 1-4 interaction between 1658 and 1672 at distance 2.655 which
> is larger than the 1-4 table size 2.400 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> Step=    0, Dmax= 1.0e-02 nm, Epot=  1.09364e+09 Fmax= 2.21154e+11,
> atom= 3292
> Step 1, time 0.001 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.680509, max 22.293625 (between atoms 1668 and 1670)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
> What is a reasonable increase in table-extension. Is this a mis-leading
> suggestion?

You should not adjust the table-extension.  The other part of the error message 
is what you need to pay attention to ("your system is exploding").

-Justin

> Here is the log from the unrestrained minimization.
> http://boinc.drugdiscoveryathome.com/_em_rcs_mdrun.txt_
> <http://boinc.drugdiscoveryathome.com/em_rcs_mdrun.txt>
> Here is a zip archive containing the working directory for this
> minimization. Its about 428 kb
> http://boinc.drugdiscoveryathome.com/rcs_ga_run_10_bt_Fzd2-MD7-MD8-7.zip_lig_24205_ChemDiv_5754-2873_ts_1263004110202172000.zip
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
>

-- 
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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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