Thanks Dan!
The issue I’m running into not is all the forces are coming up as 0 and I can’t tell what I need to change to fix the problem.
I changed the ntw etc to =1 and the nstlim = 1 ( i have tried other nstlim values and get the same results). I am running the simulation with the following, sander -O -i sim_exp.in -o sim_exp.mdout -p parameter.parm7 -y trajectory.nc -c equil.rst7 -r sim_exp.rst7 -x sim_exp.nc
to view the forces i’ve been using ncdump sim_exp.nc > sim_exp.cdl
Below, I have the input file.
>> &cntrl
>> imin=5, irest=1, ntx=5,
>> ntpr=1, ntwx=1, ntwr=1,
>> nstlim=1, dt=0.002, ntt=3,
>> tempi=298, temp0=298, tautp=2.5, ig=-1,
>> iwrap=1, ntc=2, ntf=2, ntb=1, ntwf=-1,
>> ntp=0,
>> nrespa=1,
>> ntxo=2,
>> gamma_ln=5.0, ioutfm=1,
>> /
> On Oct 30, 2018, at 9:20 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> That should work; your output trajectory should be NetCDF combined
> coordinates/forces.
>
> Note: I don't think ntwx etc work for post processing the same way
> they do for regular MD - it's either off (ntw? = 0) or on (ntw? > 0).
>
> -Dan
> On Fri, Oct 26, 2018 at 8:00 PM SARAH JEANNE LEFAVE <s.lefave.utah.edu> wrote:
>>
>> Hi all,
>>
>> I was wondering if it was possible to calculate the per-atom forces using the post-processing option with “imin=5”
>>
>> If so, what needs to be specified in your input file to get this to work. I have been using the following
>>
>> &cntrl
>> imin=5, irest=1, ntx=5,
>> ntpr=10, ntwx=10, ntwr=10,
>> nstlim=100, dt=0.002, ntt=3,
>> tempi=298, temp0=298, tautp=2.5, ig=-1,
>> iwrap=1, ntc=2, ntf=2, ntb=1, ntwf=-1,
>> ntp=0,
>> nrespa=1,
>> ntxo=2,
>> gamma_ln=5.0, ioutfm=1,
>> /
>>
>> thanks!
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 31 2018 - 11:00:03 PDT
