Hi all,
I'm trying yours ideas, but I don't know how to do this in my script:
"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 "
Have I to modify anything in my script?:
.
.
.
srun /gpfs/apps/NVIDIA/K80/AMBER/14/bin/pmemd.MPI -O -i
./min-tar/min_wat.in -p ./leap/smp-193-ptn3rig.top -c
./vcte/smp-193ptn_vcon3.mdcrd -r ./min-tar/smp-193ptn_min_wat.rst -o
./min-tar/smp-193ptn_min_wat.out -inf
./min-tar/smp-193ptn_min_wat.info -e ./min-tar/smp-193ptn_min_wat.enr
-ref ./vcte/smp-193ptn_vcon3.mdcrd
.
.
.
Have I to launch the job.sh with cpptraj?...
Thanx in advance
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 Wed Jan 08 2020 - 07:30:02 PST
