try
pmemd -O -i main etc etc
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> On Jan 18, 2021, at 19:07, Jatin Kashyap <jk435.njit.edu> wrote:
>
> [External Email]
>
> I can see one file called mden in my current directory.
> I had run the previous steps i.e. minimization & heating, in the same directory; nothing else.
>
> There are 1010 lines in that mden file. I am not able to find out whether those lines are from eq.in run or from previous.
> I can share the file here if you think it can help.
>
> Thank you.
>
> ——
> 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 7:01 PM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>>
>> You can try that, but it should work with the default. Is there a file
>> called mden in that directory with the other outputs?
>>
>>> On Mon, Jan 18, 2021, 6:48 PM Jatin Kashyap <jk435.njit.edu> wrote:
>>>
>>> Please look below for the job script.Yes, I do have the permission to
>>> write in that directory. Shall I just add -e with a file name?
>>>
>>>
>>>
>>> module unload intel
>>> module load amber
>>>
>>> pmemd -i eq.in -o eq.out -p dna.prmtop -c heat.rst -r eq.rst -x eq.mdcrd
>>> -ref heat.rst
>>>
>>> ——
>>> 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 6:43 PM, Carlos Simmerling <
>>> carlos.simmerling.gmail.com> wrote:
>>>>
>>>> please send the job script where you specified the file names.
>>>> you specify ntwe=500, which means to write energy values. The job script
>>>> will have the name of the file that you want to write energies, following
>>>> the -e flag (see the Amber manual for details). If you don't specify it,
>>>> mden is the default. Do you have permission to write in the directory
>>> where
>>>> you are running this? you might try adding -e with a file name to the
>>> pmemd
>>>> command line.
>>>>
>>>> On Mon, Jan 18, 2021 at 6:32 PM Jatin Kashyap <jk435.njit.edu> wrote:
>>>>
>>>>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__amberhub.chpc.utah.edu_analisis-2Dof-2Dnucleic-2Dacid-2Dsimulation_&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=e7FX0G4KJ5wbDog22WOJjBT1ygOUq3d6wjlvnpk5y9A&s=ODbxS0teEXWpRlzz7NfEElIuGFIN9yI4yZ8LmcnX2p4&e= <
>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__amberhub.chpc.utah.edu_analisis-2Dof-2Dnucleic-2Dacid-2Dsimulation_&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=e7FX0G4KJ5wbDog22WOJjBT1ygOUq3d6wjlvnpk5y9A&s=ODbxS0teEXWpRlzz7NfEElIuGFIN9yI4yZ8LmcnX2p4&e= >
>>>>>>>
>>>>>>> [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
>>>>>>>
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Received on Mon Jan 18 2021 - 17:00:02 PST
