I have done the constant pH 4 simulation of lysozyme.
1) I minimized the structure using restraint on backbone atom, restraint_wt = 30.0
for 3000 steps.
2) I heat the system gradualy for 1K/1ps using restraint on backbone atom,
restraint_wt = 5.0
3) Equilibration for 200ps using restraint on backbone atom, restraint_wt = 1.0
4) Production run for 10ns without restraint.
I also did the whole thing using icnstph=0 (constant protonation)to compare both
result
I processed the trajectory using ptraj and got the following result:
Heating
maximum rmsd in const pH MD - 0.98
maximum rmsd in const protonation - 2.1
Equilibration
maximum rmsd in const pH MD - 1.15
maximum rmsd in const protonation - 3.8
Production
maximum rmsd in const pH MD - 5.5 (in 5ns)
maximum rmsd in const pH MD - 10.9 (in next 5ns)
maximum rmsd in const protonation - 5 (in 5ns)
maximum rmsd in const protonation - 6 (in next 5ns)
In constant pH simulation rmsd in not stabilizing but in case of constant
protonation it is slightly stable.
why rmsd is not stabilizing upto 10ns production run can anyone help me.
Thanks With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Tue Jul 27 2010 - 03:30:03 PDT
