Pawan Kumar wrote:
probably a bad starting structure...
check this website for pressure scaling warning :
http://wiki.gromacs.org/index.php/Errors
Also,
compressibility = 4.575e-4
is of the wrong magnitude for water. Should be e-5.
-Justin
regards,
pawan
On Mon, Apr 27, 2009 at 5:21 PM, Sheetal Arora
<sheetal.aror...@gmail.com <mailto:sheetal.aror...@gmail.com>> wrote:
I am trying to run the simulation of protein ligand complex.
But after running the mdrun by giving command-"grompp –f md.
mdp –c pr.gro –p trp.top –o md.tpr "
and then "nohup mdrun –deffnm md & "
the md.log file is showing the following message-
Step 11 Warning: pressure scaling more than 1%, mu: 1.01684 1.01684
1.01684
Step 13 Warning: pressure scaling more than 1%, mu: 0.947161
0.947161 0.947161
Step 14 Warning: pressure scaling more than 1%, mu: 1.01207 1.01207
1.01207
Step 15 Warning: pressure scaling more than 1%, mu: 1.18248 1.18248
1.18248
Step 16 Warning: pressure scaling more than 1%, mu: 0.867467
0.867467 0.867467
Step 16, time 0.032 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.099556 (between atoms 1396 and 1398) rms 0.028595
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
21 23 30.8 0.1740 0.1569 0.1470
38 40 32.0 0.1740 0.1583 0.1470
54 56 33.0 0.1740 0.1588 0.1470
56 57 30.6 0.1810 0.1623 0.1530
67 69 31.4 0.1740 0.1568 0.1470
104 106 32.6 0.1740 0.1588 0.1470
106 107 31.1 0.1811 0.1632 0.1530
216 218 31.8 0.1741 0.1584 0.1470
I am attaching my md.mdp file.Please help me in this regard.
--
Sheetal Arora
M.Tech(Biotechnology & Medical Engg)
NIT Rourkela
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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