Please look for mini.in[1], heat.in[2], and eq.in[3] scripts below.
[1]
&cntrl
imin=1,
ntx=1,
irest=0,
ntpr=50,
ntf=1,
ntb=1,
cut=9.0,
nsnb=10,
ntr=1,
maxcyc=1000,
ncyc=500,
ntmin=1,
restraintmask=':1-24',
restraint_wt=25.0,
&end
&ewald
ew_type = 0,
skinnb = 1.0,
&end
[2]
&cntrl
imin=0,
ntx=1,
ntpr=500,
ntwr=500,
ntwx=500,
ntwe=500,
nscm=5000,
ntf=2,
ntc=2,
ntb=1,
ntp=0,
nstlim=50000,
t=0.0,
dt=0.002,
cut=9.0,
tempi=100.0,
ntt=1,
ntr=1,
nmropt=1,
restraintmask=':1-24',
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
[3]
&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=25000,
t=0.0,
dt=0.002,
cut=9.0,
ntt=1,
ntr=1,
irest=1,
restraintmask=':1-24',
restraint_wt=0.5,
&end
&ewald
ew_type = 0,
skinnb = 1.0,
&end
——
Jatin Kashyap
Ph.D. Student
Dr. Dibakar Datta Group
Department of Mechanical and Industrial Engineering
New Jersey Institute of Technology (NJIT)
University Heights
Newark, NJ 07102-1982
Phone- (201)889-5783
Email- jk435.njit.edu
> On Jan 18, 2021, at 6:28 PM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> I can't find any text "mden" on that tutorial page. can you include the
> actual job script for this so we can see where you defined it? mden might
> be an energy output file, and maybe you don't have permission to write? but
> we'll need to see the full script to know for sure.
>
> On Mon, Jan 18, 2021 at 6:17 PM Jatin Kashyap <jk435.njit.edu> wrote:
>
>> Dear AMBER Community,
>>
>> I am trying to reproduce the results of “Analysis of a nucleic acid
>> simulation” tutorial.[1]
>> I am facing a problem while running “eq.in” script as it's throwing an
>> error[2] even before 1st step.
>> I am using Amber 20 PMEMD 2020 on CPUs. All the scripts before this step
>> i.e. mini.in & heat.in, are running fine.
>>
>> Can somebody please point-out where I am getting it wrong.
>>
>> Thank you.
>>
>> [1]
>> https://amberhub.chpc.utah.edu/analisis-of-nucleic-acid-simulation/ <
>> https://amberhub.chpc.utah.edu/analisis-of-nucleic-acid-simulation/>
>>
>> [2]
>> Nature and format of output:
>> ntxo = 2, ntpr = 500, ntrx = 1, ntwr =
>> 500
>> iwrap = 0, ntwx = 500, ntwv = 0, ntwe =
>> 500
>> ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
>> 0
>>
>> Potential function:
>> ntf = 2, ntb = 2, igb = 0, nsnb =
>> 25
>> ipol = 0, gbsa = 0, iesp = 0
>> dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
>>
>> Frozen or restrained atoms:
>> ibelly = 0, ntr = 1
>> restraint_wt = 0.50000
>>
>> Molecular dynamics:
>> nstlim = 25000, nscm = 0, nrespa = 1
>> t = 0.00000, dt = 0.00200, vlimit = 20.00000
>>
>> Berendsen (weak-coupling) temperature regulation:
>> temp0 = 300.00000, tempi = 0.00000, tautp = 0.20000
>>
>> Pressure regulation:
>> ntp = 1
>> pres0 = 1.00000, comp = 44.60000, taup = 0.20000
>>
>> SHAKE:
>> ntc = 2, jfastw = 0
>> tol = 0.00001
>>
>> | Intermolecular bonds treatment:
>> | no_intermolecular_bonds = 1
>>
>> | Energy averages sample interval:
>> | ene_avg_sampling = 500
>>
>> Extra-points options:
>> frameon = 1, chngmask= 1
>>
>> Ewald parameters:
>> verbose = 0, ew_type = 0, nbflag = 1, use_pme =
>> 1
>> vdwmeth = 1, eedmeth = 1, netfrc = 1
>> Box X = 62.425 Box Y = 62.425 Box Z = 62.425
>> Alpha = 109.471 Beta = 109.471 Gamma = 109.471
>> NFFT1 = 64 NFFT2 = 64 NFFT3 = 64
>> Cutoff= 9.000 Tol =0.100E-04
>> Ewald Coefficient = 0.30768
>> Interpolation order = 4
>>
>> LOADING THE CONSTRAINED ATOMS AS GROUPS
>>
>>
>> 5. REFERENCE ATOM COORDINATES
>>
>> default_name
>> Mask :1-24; matches 758 atoms
>> | EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 15575 0
>> | EXTRA_PTS, trim_bonds: num bonds AFTER trim = 15575 0
>> | EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 5645 0
>> | EXTRA_PTS, trim_bonds: num bonds AFTER trim = 544 0
>> | EXTRA_PTS, trim_theta: num angle BEFORE trim = 640 0
>> | EXTRA_PTS, trim_theta: num angle AFTER trim = 640 0
>> | EXTRA_PTS, trim_theta: num angle BEFORE trim = 836 0
>> | EXTRA_PTS, trim_theta: num angle AFTER trim = 836 0
>> | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 1390 0
>> | EXTRA_PTS, trim_phi: num diheds AFTER trim = 1390 0
>> | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 1756 0
>> | EXTRA_PTS, trim_phi: num diheds AFTER trim = 1756 0
>>
>>
>> --------------------------------------------------------------------------------
>> 3. ATOMIC COORDINATES AND VELOCITIES
>>
>> --------------------------------------------------------------------------------
>>
>> default_name
>> begin time read from input coords = 100.000 ps
>>
>>
>> Unit 15 Error on OPEN: mden
>>
>> ——
>> Jatin Kashyap
>> Ph.D. Student
>> Dr. Dibakar Datta Group
>> Department of Mechanical and Industrial Engineering
>> New Jersey Institute of Technology (NJIT)
>> University Heights
>> Newark, NJ 07102-1982
>> Phone- (201)889-5783
>> Email- jk435.njit.edu
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Mon Jan 18 2021 - 16:00:02 PST
