(I forgot to add [AMBER] in subject so I resend this email. Hope I didn't
cause any confusion.. Thanks!)
Hi all!
recently I want to do multiple independent runs by assigning different
velocities to each run.
So I have three stages for each run, eq1 for heating up, eq2 for pressure
relaxation, and then run at NPT conditions. The assignment of velocites is
at eq1 stage and below is the input:
*Heating up the system equilibration stage -- only water is mobile*
* &cntrl*
* nstlim=100000, dt=0.002, ntx=1, irest=0, ntpr=500, ntwr=5000, ntwx=500,*
* tempi =0.0, temp0=300.0, ntt=1, tautp=2.0, ig=-1,*
* ntb=1, ntp=0,*
* ntc=2, ntf=2,*
* nrespa=1,*
* ntr=1,*
* iwrap=1,*
*/*
*Keep protein and ligand fixed*
*50.0*
*RES 1 100*
*END*
*END*
However, I noticed that each run are IDENTICAL in all .out, .crd, and .rst
files. So I realize the ig flag didn't work at all. Maybe I didn't fully
understand the sentence in manual "The MD starting velocity is dependent on
the random number generator seed if NTX .lt. 3 .and. TEMPI .ne. 0.0." Can
anybody help illustrate how to correctly use ig flag? It seems ig=-1
doesn't work if I have ntt=1 and tempi=0.0...? So in my case, what's the
best way to assign random velocities in each run? How about assigning a
number to ig? Do I need to change it for each run? It should be a very
simple one but I have no experience dealing with it before.. Thanks for
your time!
Best,
Guqin
--
Guqin SHI
The Ohio State University
College of Pharmacy
500 W. 12th Ave.
Columbus, OH, 43210
(614)688-3531
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Received on Fri Oct 16 2015 - 09:30:04 PDT
