Dear Amber Experts,
I am trying to perform MD simulations in amber20 on GPU (pmemd.cuda). Here
is the production input file I am using:
simann with pos-restraint on receptor + dist restraint on ligand
&cntrl
ntwx = 100,
ntwe = 100, ntwr = 50, ntpr = 1000, ntxo = 1, ioutfm = 0,
imin = 0,
ntx = 1,
temp0 = 300,
tempi = 300,
ig = -1,
nstlim = 20000,
dt = 0.002,
ntb = 0,
nscm = 100,
ntc = 2, ntf = 2,
ntt = 2, vrand = 1000,
igb = 1, cut = 999.0,
nmropt = 1,
restraintmask = ':1-X_LASTREC_RESIDNO_X & !.H= ',restraint_wt = 100,
ntr = 1,
/
&wt type='END', /
DISANG=./restraints.in
My restraints.in file looks like this:
# LIG119.CA DUM120.D1
&rst
iat=1620,1625,
ialtd=0, r1= 0, r2= 0.1, r3= 15, r4= 15.1,
rk2=500.0, rk3=500.0 ,
/
When I look at the output log file, I find the following:
Thu Jul 28 16:34:07 EDT 2022
My PID is 30783
rec.HIS.1929.1
staring minimization 16:34:08
after 05mi: 16:34:27
starting md run 16:34:27
| WARNING :: The NMR distance restraint between atoms 9524 and 4574 could
| be stretched to an unsafe degree. The run will proceed, but
| overflow in the force accumulation is possible.
after md: 16:34:37
after pdb: 16:34:43
rec.HIS.1929.1.rst 16:34:07 16:34:43
Is the warning message suggesting that something is wrong during this stage
of the simulation? Please advise how to proceed.
Respectfully yours,
Prithviraj Nandigrami
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Received on Thu Aug 04 2022 - 13:37:35 PDT
