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 - 05:00:05 PST
