Hello everyone,
I have a simple question - sorry if it is too trivial for this mailing list.
I am doing umbrella sampling (in Amber10) using dihedral angle restraints -
my mdin file looks like this:
=====
* &cntrl*
* imin = 0,*
* nmropt = 1,*
* irest = 1,*
* ntx = 7,*
* ntb = 1,*
* cut = 8.6*
* ntr = 0,*
* ntc = 2,*
* ntf = 2,*
* tempi = 300.0,*
* temp0 = 300.0,*
* ntt = 3,*
* gamma_ln = 1.0,*
* ig = -1,*
* nstlim = 200, dt = 0.001,*
* ntpr = 200, ntwx = 10, ntwr = 200*
* igb = 0,*
* /*
* &wt type='DUMPFREQ', istep1=10 /*
* &wt type='END' /*
* DISANG=psi.RST*
* DUMPAVE=psi_vs_t*
*====*
I know that the *psi_vs_t* file contains the values of the restrained
dihedral angle.
Just as a check, I computed the same dihedral angle values using *ptraj*and the
*mdcrd *file. I am getting similar, but different values than what is in *
psi_vs_t*. The frequency of output is the same for both files, so I would
have thought that they would match. I find this somewhat unnerving and was
wondering if perhaps I am misunderstanding something.
Thank you very much.
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Received on Wed Mar 07 2012 - 14:30:02 PST
