Dynamics restrt files would have velocities.
Bill
On 12/12/19 1:13 AM, MYRIAN TORRES RICO wrote:
> Thank you a lot!! I'm going to probe your ideas, and I hope to work.
> The global idea was to carry out a second molecular dynamics more
> shorter with restrictions to correct the molecular dynamics previous,
> so that's why I need my final file as a restart file.
>
>
> Myriam
>
>
> Bill Ross <ross.cgl.ucsf.edu> escribió:
>
>> When minimizing, there are no velocities.
>>
>> Bill
>>
>> On 12/11/19 9:36 AM, James Kress wrote:
>>> Is there any particular reason the restart files do not contain velocities?
>>> It seems to me that a "true restart" would need to have coordinates and
>>> velocities to accurately continue an interrupted run?
>>>
>>> What am I not understanding?
>>>
>>> Jim
>>>
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>>> -----Original Message-----
>>> From: David A Case <david.case.rutgers.edu>
>>> Sent: Wednesday, December 11, 2019 11:41 AM
>>> To: AMBER Mailing List <amber.ambermd.org>
>>> Subject: Re: [AMBER] error
>>>
>>> On Wed, Dec 11, 2019, MYRIAN TORRES RICO wrote:
>>>> Exactly, I want to run pmemd using final trayectory (.mdcrd) instead
>>>> firsts coordinates (.crd).
>>> You can't do this (directly): trajectory files have lots of coordinates
>>> (frames) in them, whereas a restart file has only one set of coordinates.
>>> pmemd doesn't know how to start from a trajectory file.
>>>
>>> Do you have a "final" restart file (created with the "-r" flag)? Might that
>>> not be what you want here, as a starting point for the next MD segment?
>>>
>>> If not, do this: use cpptraj, with trajin being the trajectory file:
>>> choose the frame you wish to use. Set trajout to write a restart file.
>>>
>>> Then you can use the restart file you just created. It won't have any
>>> velocities, so you will have to set ntx=1 and tempi to the initial
>>> temperature you want.
>>>
>>> ....hope this helps....dac
>>>
>>>
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Received on Thu Dec 12 2019 - 11:30:02 PST
