Hi,
You are not actually running CpHMD in your equilibration script (md.in), so
you are not going to generate a cprestrt file.
You do not need to add -cpin 3LZT.solv10.cpin -cpout
3LZT.solv10.equil.cpout -cprestrt 3LZT.solv10.equil.cpin when running the
equilibration.
Eric
On 10 February 2017 at 14:40, Tsibela German Tebello Mofokeng <
1754789.students.wits.ac.za> wrote:
> Dear Amber users
>
> Iam trying to run explicit solvent CpHMD calculations as outlined in
> tutorial: http://jswails.wikidot.com/explicit-solvent-constant-ph-md
>
> I managed to get all the output files for the minimization and heating
> steps, I tried to run the equilibration step but I cannot get the
> *-cprestrt* *.cpin* file form the equilibration step. What could be the
> problem?
>
> The calculation only produced the following files: .mdout, cpout,.nc and
> rst7
>
> I used the following commands:
>
> mpirun -np 24 -machinefile $PBS_NODEFILE $exe -O -i md.mdin -p
> 3LZT.solv10.parm7 -c 3LZT.solv10.heat.rst7 -cpin 3LZT.solv10.cpin -o
> 3LZT.solv10.equil.mdout -cpout 3LZT.solv10.equil.cpout -r
> 3LZT.solv10.equil.rst7 -cprestrt 3LZT.solv10.equil.cpin -x
> 3LZT.solv10.equil.nc
>
> md.in script:
>
> Explicit solvent molecular dynamics constant pressure MD
> &cntrl
> imin=0, irest=1, ntx=5,
> ntpr=1000, ntwx=1000, nstlim=2000000,
> dt=0.002, ntt=3, tempi=300,
> temp0=300, gamma_ln=1.0, ig=-1,
> ntp=1, ntc=2, ntf=2, cut=8,
> ntb=2, iwrap=1, ioutfm=1,
> /
>
>
> Thank you
> Tebello
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>
--
Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
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Received on Fri Feb 10 2017 - 07:00:03 PST
