Dear amber users
I was doing implicit solvent (GB version2) MD simulation on my peptide
and the peptide with the ligand but the RMSD is not getting
stabilized. I run it at different simulation times to see if it is
getting stabilized (from 100ps to 10 ns).
I am suspecting that there could be a problem with my approach? I
followed tutorial 1 for the DNA
The peptide is first minimized according to:
Minimisation
&cntrl
imin = 1,
maxcyc = 1000,
ncyc = 500,
ntb = 0,
igb = 2
cut = 12
/
The input file for the simulation is:
MD run Generalised Born, 12 angstrom cut off
&cntrl
imin = 0, ntb = 0,
igb = 2, ntpr = 100, ntwx = 100,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0
nstlim = 50000000, dt = 0.001,
cut = 12.0
/
If you notice any mistake in the method I am using, please tell me.
With best regards
Thank you
Workalemahu
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Received on Fri Jul 10 2009 - 10:10:55 PDT
