you need ntWx set to a number lower than nstlim. try setting it to 100 maybe
Sent from my iPad
> On Jan 6, 2021, at 09:58, K Jan <10dunajkr.gmail.com> wrote:
>
> [External Email]
>
> This is the input : (
> &cntrl
> ntf=2, ntb=1, cut=12.0,
> nstlim=5000, dt=0.002,
> tempi=0.0,temp0=100.0, ntt=1,
> ntc=2,
> imin=0, irest=0, ntx=1,
> ntr=1,
> restraint_wt=50.0,
> restraintmask=':1-32'
> &end )
>
> I have ntx =1 so that shouldn`t be a problem
>
>> On Wed, 6 Jan 2021 at 14:26, Carlos Simmerling <carlos.simmerling.gmail.com>
>> wrote:
>>
>> can you provide your input file md1.in?
>> it may be that your ntwx is not set to output snapshots to the trajectory
>> file.
>>
>>> On Wed, Jan 6, 2021 at 7:58 AM K Jan <10dunajkr.gmail.com> wrote:
>>>
>>> Dear all amber users
>>>
>>>
>>> I have been simulating a molecule on Amber and I was wondering whether I
>>> could ask you a question as I am unsure of how to visualize my molecule
>>> with the output files that I have received from my sander code.
>>>
>>> I`ve completed analysis on the molecule by calculating the density,
>> volume,
>>> pressure , radius of gyration and the Root Mean Square Deviation.
>>>
>>> I would like to use vmd to view the molecule at the different times of
>> the
>>> simulation ( simulation lasted 80 picoseconds , and it was completed in
>>> steps of 10ps) . However, I don`t have any trajectory output files so I
>> am
>>> not sure how to do this.
>>>
>>> This is my sander code:
>>>
>>> sander -O -i md1.in -o md1KCL.out -inf md1KCL.inf -c lr16wKCL.k.minw2
>> -ref
>>> lr16wKCL.k.minw2 -r lr16wKCL.k.md1 -p lr16wKCL.k.top -x lr16wKCL.k.md1.x
>> -e
>>> lr16wKCL.md1.ene &
>>>
>>> and the output files I get are:
>>>
>>> lr16wKCL.k.md1, md1KCL.inf and md1KCL.out
>>>
>>>
>>> I have also tried running the code by using lr16KCL.k.nc after -x but
>> this
>>> doesn’t work either.
>>>
>>> I need lr16wKCL.k.md1.x in order to view the molecule in the vmd but for
>>> some reason this code doesn’t output this trajectory file.
>>>
>>> Unless, does the lr16wKCL.k.md1 output file contain the trajectory and
>> can
>>> I use this in lieu of the explicit trajectory file ?
>>>
>>>
>>> many thanks,
>>>
>>>
>>> Kris J Duna
>>>
>>>
>>> --
>>> null
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Received on Wed Jan 06 2021 - 07:30:03 PST
