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
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