Dear AMBER Experts,
I am facing an issue while running nucleic acid simulations that I am not
sure the origin of. The minimization simulation runs fine using the follow
input file:
Minimzing the system
with 25 kcal/mol restraints
on RNA, 500 steps of steepest
descent and 500 of
conjugated gradient
&cntrl
imin=1,
ntx=1,
irest=0,
ntpr=50,
ntf=1,
ntb=1,
cut=9.0,
nsnb=10,
ntr=1,
maxcyc=10000,
ncyc=5000,
ntmin=1,
restraintmask=':1-67',
restraint_wt=25.0,
&end
&ewald
ew_type = 0, skinnb = 5.0,
&end
In the heating step, it crashes and the subsequent runs crash as well. Here
is the heating input file:
Heating the system with 25 kcal/mol
restraints on RNA, V=const
&cntrl
imin=0, ntx=1, ntpr=500,
ntwr=500, ntwx=500, ntwe=500,
nscm=5000,
ntf=2, ntc=2,
ntb=1, ntp=0,
nstlim=1000, t=0.0, dt=0.002,
cut=9.0,
tempi=100.0, ntt=1,
ntr=1,nmropt=1,
restraintmask=':1-67',
restraint_wt=25.0,
&end
&wt type='TEMP0',istep1=0,
istep2=5000, value1=100.0,value2=300.0,
&end
&wt type='TEMP0',istep1=5001,
istep2=50000, value1=300.0,value2=300.0,
&end
&wt type='END', &end
and the subsequent equilibration input file:
Equilibrating the system
with 0.5 kcal/mol restraints
on RNA, during 500ps, at
constant T= 300K & P=1ATM
and coupling = 0.2
&cntrl
imin=0, ntx=5, ntpr=500,
ntwr=500, ntwx=500,
ntwe=500,
nscm=5000,
ntf=2, ntc=2,
ntb=2, ntp=1, tautp=0.2,
taup=0.2,
nstlim=1000000,
t=0.0, dt=0.002,
cut=9.0,
ntt=1,
ntr=1,
irest=0,
restraintmask=':1-67',
restraint_wt=0.5,
&end
&ewald
ew_type = 0, skinnb = 5.0,
&end
I get the following error message after the minimization step:
*STOP PMEMD Terminated Abnormally!srun: error: gpu02.local: task 0: Exited
with exit code 1Unmatched '.*
*| ERROR: I could not find enough velocities in mini.rst7*
I am not sure what the source of this error is but in the AMBER archive it
is mentioned to use irest = 0 and increase the value of skinnb (which I set
to 5) but that did not help.
Any help/guidance would be much appreciated.
Sincerely,
PN
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Received on Tue Jan 24 2023 - 12:00:06 PST
