> On Jul 17, 2015, at 3:12 AM, Albert <mailmd2011.gmail.com> wrote:
>
> Hello:
>
> I've produced 3 round of 1 ns MD for MMPBSA calcualtion, each of then
> contains 100 frames. Here is my setting:
>
> production
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=500000,dt=0.002,
> ntc=2,ntf=2,
> cut=9.0, ntb=2, ntp=1, taup=2.0,
> ntpr=5000, ntwx=5000,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> /
>
> so if I use the following mmpbsa.in for mmpbsa.py:
>
> &general
> endframe=100, verbose=1,
> /
> &gb
> igb=2, saltcon=0.150
> /
> &pb
> istrng=0.150, fillratio=4.0
> /
>
> I am just wondering how many frames in all would be calculated? 100
> frames or 300 frames? I am a little bit confused for that.
I think it should be 100. In older versions of MMPBSA.py, the endframe would be applied separately to each trajectory. But now it treats all frames as one long trajectory and applies endframe to that set of frames.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jul 17 2015 - 13:00:03 PDT
