So, I will use the same -p 3LZT.solv10.parm7 and -c 3LZT.solv10.equil.rst7
files for all md calculations at different pH values similar to toturial 18
on implicit solvent?
Yes
Should I used the 3LZT.solv10.cpin as (-cpin) file generated from the
initial parm7 file for the 1st CpHMD at pH_0 and the -cprestrt .cpin file
generated from CpHMD at pH_0 for (-cpin) in the following CpHMD at pH_1?
No you should use the same original cpin file when starting each
simulations: i.e. 3LZT.solv10.cpin when you start your simulations at pH 0,
at pH 1, ... the cprestrt cpin file is only when you continue a specific
CpHMD.
Regards
Tebello
Cheers,
Eric
On 10 February 2017 at 16:56, Eric Lang <eric.lang.bristol.ac.uk> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> Eric Lang
>
> BrisSynBio Postdoctoral Research Associate Modelling
> Centre for Computational Chemistry
> School of Chemistry - University of Bristol
> Bristol BS8 1TS - United Kingdom
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Feb 10 2017 - 13:30:03 PST
