[gmx-users] Unstable Minimizations

[Jack Shultz]

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 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?
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100110/a07a27d1/attachment.html>