AMBER Archive (2008)

Subject: AMBER: AMBER : Inconsistent MD length and no of angles after ptraj

From: parul sharma (
Date: Fri Nov 07 2008 - 03:52:07 CST

Dear all,

I run my GB calculations for 35ns 1.e 35000 ps, the input i used was:

 imin = 0,
 ntc=2, ntf=2,
 cut=12.0, igb=2, saltcon=0.2, gbsa=1,
 nstlim=5000000, dt=0.001,
 ntt=1, tempi=0.0, temp0=300.0, tautp=1.0,
 ntx=5, irest=1, ntb=0,
 ntpr = 500, ntwx = 500, ntwr = 500, ntwe = 500, nscm=1000,
and after obtaining the crd files, i did ptraj analysis upto 35000 ps, but i
am getting 70000 conformations or angles for all phi, psi and omegas. It's
just double the length of my MD simulation, i am not sure weather i should
get the same number of angles, as in 35000 or double which i am getting.
Also i checked for the duplication of the angles after 35000 nsc but all
angles i am getting are different. Please help me out.

Parul Sharma
PhD Student, Durban University of Technology,
South Africa

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