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 - 01:30:02 PST
