[gmx-users] problem in analyzing

hazizian hazizian at razi.tums.ac.ir
Sat Dec 20 09:58:10 CET 2008

I want to analyze md. This md took 10 ns(10000 ps) for a protein with 206 
residue and 2 Mn plus about 17000 molecule solvent as water.
then I construct extra group containig Protein+2 Mn with make_ndx comand.
I did g_rmsf for extracting the average structure of the new group rmsd 
equilibrated section :

g_rmsf -n p+mn.ndx -s md300.tpr -f md300.trr -b 9000 -e 10000 -ox e.pdb              
then I did procheck to evaluate e.pdb, the summery of ramachandran was:

83.3% core 15.2% allow 0.5% gener 1% disall  G-factor= -0.75

for improving this result I did energy minimization with steepest descent 
and cg. the parameter for steep is emtol=1000 the ramachandran result was:

82.8% core 15.7% allow 0% gener 1.5% disall  G-factor= -0.3

steep emtol=10:
76% core 22.1% allow 0.5% gener 1.5% disall  G-factor= -0.47

after performing cg nstcgstep= 9000 emtol=1 nstep=0.01 the result was
76% core 21.6% allow 1% gener 1.5% disall  G-factor= -0.48

it seems that the results get worse after doing EM.
my question is why  performing EM worse this result? 
what could I to improve ramachandran result, is it better to do md for 
longer time(according to 206 residue)?
another question is whether incresing tempreture from 300 to 500 or greater 
affect procheck result or not? besids changing temprature and nstep 
parameter in md.mdp with chaning in which parameter can we improve md 
thank's for replying.

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