Maybe it is using too much memory? I haven't used cpptraj, so you may
need a developer's help.
cpptraj should print a message if there is a problem.
On 11/13/17 5:03 AM, Rana Rehan Khalid wrote:
> I think the error occur because every time my simulation end due to low
> space its not ends properly always number of steps in my .in file 1000000
> while every time it ends with 728000 steps may me due to this number of
> frame not determined and i ran it again from the previous restart file.
> kindly guide if i am thinking wrong.
>
> On Mon, Nov 13, 2017 at 5:41 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> wrote:
>
>> It ran 728100 steps and size is 2.1gb
>>
>> On Mon, Nov 13, 2017 at 5:39 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>
>>> How big is md1.mdcrd.gz?
>>>
>>>
>>> On 11/13/17 4:36 AM, Rana Rehan Khalid wrote:
>>>> Sir this is the .in file which i use to run MD simulation.
>>>> Production
>>>> &cntrl
>>>> imin=0,
>>>> ntx=5,
>>>> irest=1,
>>>> nstlim=1000000,
>>>> dt=0.002,
>>>> ntf=2,
>>>> ntc=2,
>>>> temp0=300.0,
>>>> ntpr=100,
>>>> ntwx=100,
>>>> cut=8.0,
>>>> ntb=2,
>>>> ntp=1,
>>>> ntt=3,
>>>> gamma_ln=2.0,
>>>> ig=-1,
>>>> /
>>>>
>>>> On Mon, Nov 13, 2017 at 5:32 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
>>>> wrote:
>>>>
>>>>> CPPTRAJ: Trajectory Analysis. V17.00
>>>>> ___ ___ ___ ___
>>>>> | \/ | \/ | \/ |
>>>>> _|_/\_|_/\_|_/\_|_
>>>>>
>>>>> | Date/time: 11/13/17 17:30:53
>>>>> | Available memory: 3.696 GB
>>>>>
>>>>> Loading previous history from log 'cpptraj.log'
>>>>>> parm bay.prmtop
>>>>> Reading 'bay.prmtop' as Amber Topology
>>>>> Radius Set: modified Bondi radii (mbondi)
>>>>>> list parm
>>>>> PARAMETER FILES (1 total):
>>>>> 0: bay.prmtop, 30230 atoms, 9254 res, box: Orthogonal, 9069 mol, 9053
>>>>> solvent
>>>>>> trajin md1.mdcrd.gz
>>>>> Reading 'md1.mdcrd.gz' as Amber Trajectory
>>>>> Warning: md1.mdcrd.gz: Number of frames in compressed traj could not be
>>>>> determined.
>>>>> Warning: Frames will be read until EOF.
>>>>>> list trajin
>>>>> INPUT TRAJECTORIES (1 total):
>>>>> 0: 'md1.mdcrd.gz' is an AMBER trajectory, Parm bay.prmtop (Orthogonal
>>>>> box), unknown #frames, start=0 offset=1
>>>>> Total number of frames is unknown.
>>>>>
>>>>> On Mon, Nov 13, 2017 at 5:30 PM, Rana Rehan Khalid <rrkhalid.umich.edu
>>>>> wrote:
>>>>>
>>>>>> No it gives error immediately. It did not run for any length.
>>>>>>
>>>>>> On Mon, Nov 13, 2017 at 5:24 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>>>>>
>>>>>>> Did it run for any length of time? Was the cpu busy? Was there any
>>> other
>>>>>>> output?
>>>>>>>
>>>>>>>
>>>>>>> On 11/13/17 4:22 AM, Rana Rehan Khalid wrote:
>>>>>>>> yes sir program is stop.
>>>>>>>>
>>>>>>>> On Mon, Nov 13, 2017 at 4:33 PM, Bill Ross <ross.cgl.ucsf.edu>
>>> wrote:
>>>>>>>>> Do you see the cpu in use from the program?
>>>>>>>>>
>>>>>>>>> $ top
>>>>>>>>>
>>>>>>>>> Bill
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 11/13/17 3:32 AM, Rana Rehan Khalid wrote:
>>>>>>>>>> No its not stop . One maybe issue i am not sure that I ran the
>>>>>>> simulation
>>>>>>>>>> on amber 14 which is install on our cluster while in my laptop it
>>> is
>>>>>>>>> amber
>>>>>>>>>> 17 and I start analysis on my laptop. Thanks
>>>>>>>>>>
>>>>>>>>>> On Mon, Nov 13, 2017 at 4:26 PM, Bill Ross <ross.cgl.ucsf.edu>
>>>>>>> wrote:
>>>>>>>>>>> Did the program stop? Was there any other output?
>>>>>>>>>>>
>>>>>>>>>>> Bill
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 11/13/17 3:24 AM, Rana Rehan Khalid wrote:
>>>>>>>>>>>> Dear Amber users
>>>>>>>>>>>>
>>>>>>>>>>>> I am facing this error. I have just started the analysis on my
>>>>>>> mdcrd
>>>>>>>>>>> files
>>>>>>>>>>>> and face this issue kindly guide how can i resolve it. I already
>>>>>>> run
>>>>>>>>> the
>>>>>>>>>>> 20
>>>>>>>>>>>> ns simulation and now start its analysis when i open the first
>>> file
>>>>>>>>> these
>>>>>>>>>>>> warning messages show.
>>>>>>>>>>>>
>>>>>>>>>>>> parm bay.prmtop
>>>>>>>>>>>> Reading 'bay.prmtop' as Amber Topology
>>>>>>>>>>>> Radius Set: modified Bondi radii (mbondi)
>>>>>>>>>>>>> trajin md1.mdcrd.gz
>>>>>>>>>>>> Reading 'md1.mdcrd.gz' as Amber Trajectory
>>>>>>>>>>>> Warning: md1.mdcrd.gz: Number of frames in compressed traj could
>>>>>>> not be
>>>>>>>>>>>> determined.
>>>>>>>>>>>> Warning: Frames will be read until EOF.
>>>>>>>>>>>>> list
>>>>>>>>>>>> trajin
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> INPUT TRAJECTORIES (1 total):
>>>>>>>>>>>> 0: 'md1.mdcrd.gz' is an AMBER trajectory, Parm bay.prmtop
>>>>>>>>> (Orthogonal
>>>>>>>>>>>> box), unknown #frames, start=0 offset=1
>>>>>>>>>>>> Total number of frames is unknown.
>>>>>>>>>>>>
>>>>>>>>>>>> Regards
>>>>>>>>>>>> _______________________________________________
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Received on Mon Nov 13 2017 - 06:00:06 PST
