Dear Amber users
I generated the mutant models (a dimer structure), Most of these mutant
models md runs are fine but some models failed during heating, I checked
the earlier threads
following things I have applied
1. I ran the annealing through pmemd.cuda and then also try it with sander
2. I also follow this thread
http://archive.ambermd.org/201004/0189.html
3. I also used H++ to make my initial structure good. I also used the pqr
file of this complex. I thought maybe the initial structure was not good.
but facing the same error. My error is
vlimit exceeded for step 1; vmax = 74.4479
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 1059 805 804
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
I used this input file for heating
Heat
&cntrl
imin=0,
ntx=1,
irest=0,
nstlim=50000,
dt=0.002,
ntf=2,
ntc=2,
tempi=0.0,
temp0=300.0,
ntpr=1000,
ntwx=1000,
cut=10.0,
ntb=1,
ntp=0,
ntt=3,
gamma_ln=2.0,
nmropt=1,
ig=-1,
/
&wt type='TEMP0', istep1=0, istep2=9000, value1=0.0, value2=300.0 /
&wt type='TEMP0', istep1=9001, istep2=10000, value1=300.0, value2=300.0 /
&wt type='END' /
Kindly guide me how I can resolve this issue.
Thank you for your time in advance.
Best
Rehan
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Received on Thu Jul 15 2021 - 14:00:02 PDT
