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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>
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Received on Mon Nov 13 2017 - 05:00:04 PST
