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 - 05:00:06 PST
