2010/4/8 Yunfen Wang <wangfen041237.163.com>:
> Hello,
> This my input file :
>
> 1ns MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 0.5,
> iwrap = 1，
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> tautp = 0.10000,ntt = 1,
> nstlim = 2000000, dt = 0.0005,
You are SHAKEing the hydrogen bonds (ntf=2, ntc=2), yet you are taking
a shorter time step (0.5 femtoseconds) than you'd need if you weren't
SHAKEing. This doesn't directly address your issue, but it is
something worth pointing out.
> ntpr = 500, ntwx = 500, ntwr = 500
> /
> I am doing MD simulation for Protein in different solvents to research solvation effect . Before this i have done minmization and heating for the system .
>
> I donn't know what is wrong ? Thank you for help .
>
My suggestion -- take your last known good restart file (one where
there is no ****s present, and one where you didn't delete anything
from it), and run a short MD simulation with iwrap=1. Then visualize
the system with your favorite program to see if iwrap is not mapping
some atom back into the primary cell. Of course, you should have
already visualized your restart files to see if that could help you
debug at all.
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Apr 08 2010 - 19:00:05 PDT
