[gmx-users] About generating step files

[Kirti Patel]

Dear All,

I am doing simulated annealing of a 16mer peptide. It is done in 2 steps, the first step consists
of racemisation which I do by changing gi_2 and ga_12 factors in *bon.itp files. But while doing
so in simulation at high temperature step files are generated with a warning of LINCS. Do anybody
know how to avoid this and run the heating cycle smoothly.

The warning is as follows

Step 31359, time 31.359 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.027907 (between atoms 2 and 3) rms 0.003864
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 31360, time 31.36 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 5.000147 (between atoms 2 and 3) rms 0.544310
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
      1      2   91.1    0.1531   0.1461      0.1530
      2      3   90.1    0.1196   0.7380      0.1230
      2      4   88.2    0.1310   0.4803      0.1330
      4      5   96.0    0.1010   0.1742      0.1000
      4      6   92.6    0.1468   0.6176      0.1470
      6      7   87.8    0.1553   0.4581      0.1530
      6     11   83.2    0.1543   0.3369      0.1530
     11     12   95.6    0.1252   0.2177      0.1230
     11     13  112.7    0.1360   0.1504      0.1330
Wrote pdb files with previous and current coordinates
step 31360, will finish at Tue Jun 28 10:42:39 2005
Step 31361, time 31.361 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 45.440052 (between atoms 23 and 24) rms 5.917597
bonds that rotated more than 30 degrees:

Waiting for reply.

Thanks in advance.

-- 
Kirti Patel

"Research Scholar"
Bio-organic Lab,
Department of Chemistry,
Indian Inst. of Technology Bombay
Ph. No.-022-25764780(Lab),
        022-25764168(Lab)
Fax No:-022-25767152