Dear all,
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
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,
Durban,
South Africa
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Fri Dec 05 2008 - 11:12:32 PST
