AMBER Archive (2008)

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

From: David A. Case (
Date: Fri Nov 07 2008 - 23:33:48 CST

On Fri, Nov 07, 2008, parul sharma wrote:
> I run my GB calculations for 35ns 1.e 35000 ps, the input i used was:
> &cntrl
> imin = 0,
> ntc=2, ntf=2,
> cut=12.0, igb=2, saltcon=0.2, gbsa=1,
> ntpr=50,
> 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,
> &end

The input above is for 5ns, and would generate 10000 snapshots. It's not
clear how you created the "35ns" trajectory.

If you (say) did 7 such runs, then you would have 35 ns of trajectories,
saved at 0.5ps intervals, for a total of 70000 snapshots. If you computed an
angle for each snapshot, you would get 70000 numbers, which sounds like what
you report. But I'm really guessing here: you didn't really report enough
information to allow me to be sure of anything.

> i did ptraj analysis upto 35000 ps,

Since you didn't give the ptraj inputs, it's pretty hard to tell what is going
on. Ptraj will tell you how many snapshots you have, which may help.


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