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 - 05:30:05 PST
