On 5/8/13 3:07 AM, Subramaniam Boopathi wrote:
Dear Sir,
I am succesfully run molecules upto energy minimization, in case of
position restrain md step , i have following, could you help to overcome
the A charge group moved too far between two domain decomposition steps.
Step 1, time 0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.021061, max 0.387149 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
360 363 90.0 0.0960 0.1332 0.0960
Step 2, time 0.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.034712, max 0.636602 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
360 363 90.1 0.1332 0.1571 0.0960
Back Off! I just backed up step2b_n7.pdb to ./#step2b_n7.pdb.1#
Back Off! I just backed up step2c_n7.pdb to ./#step2c_n7.pdb.1#
Wrote pdb files with previous and current coordinates
Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.023755, max 0.423951 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
360 363 90.0 0.1571 0.1367 0.0960
Step 4, time 0.008 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.051081, max 0.931870 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
360 363 90.3 0.1367 0.1855 0.0960
Back Off! I just backed up step4b_n7.pdb to ./#step4b_n7.pdb.1#
Back Off! I just backed up step4c_n7.pdb to ./#step4c_n7.pdb.1#
Wrote pdb files with previous and current coordinates
Step 5, time 0.01 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.020335, max 0.372790 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
360 363 89.9 0.1855 0.1318 0.0960
Step 6, time 0.012 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.056021, max 1.029913 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
360 363 90.2 0.1318 0.1949 0.0960
Back Off! I just backed up step6b_n7.pdb to ./#step6b_n7.pdb.2#
Back Off! I just backed up step6c_n7.pdb to ./#step6c_n7.pdb.2#
Wrote pdb files with previous and current coordinates
Step 7, time 0.014 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.024586, max 0.451876 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
360 363 90.0 0.1949 0.1394 0.0960
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-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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