Dear amber !
It is working , the mistake is mine ! , when I give the run as
pmemd.cuda -i eq2_pmemd.in -p solvated_protein.prmtop -c eq1.rst -ref
eq1.rst -o eq2.log
I was able to do it and if i give the mdcrd and rest file flags it is
giving me the problem.
I also understood that the default value for nrespa=1.
thank you so much for the reply , but still I have some issues on
equilibration when i run in CUDA the error is as follows
*****************
ERROR: Calculation halted. Periodic box dimensions have changed too much
from their initial values.
Your system density has likely changed by a large amount, probably from
starting the simulation from a structure a long way from equilibrium.
[Although this error can also occur if the simulation has blown up for
some reason]
The GPU code does not automatically reorganize grid cells and thus you
will need to restart the calculation from the previous restart file.
This will generate new grid cells and allow the calculation to continue.
It may be necessary to repeat this restarting multiple times if your
system
is a long way from an equilibrated density.
Alternatively you can run with the CPU code until the density has
converged
and then switch back to the GPU code.
************************
SO I have ro run the equilibration in CPU based sander.MPI and I can run
the MD using CUDA will this fix the issues or what I should do
thank you
On Wed, Sep 2, 2015 at 3:09 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Lara,
>
> Can you send me - directly to me and NOT to the list - the following file
> please:
>
> $AMBERHOME/src/pmemd/src/mdin_ctrl_dat.F90
>
> Thanks,
>
> All the best
> Ross
>
> > On Sep 2, 2015, at 12:04 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> >
> > Hi Lara,
> >
> > I think something is VERY wrong with your AMBER installation here. What
> version of AMBER are you using, do you know what patches were applied and
> how it was compiled?
> >
> > Do the test cases pass after installation?
> >
> > The default for nrespa should be 1.0 and so if it is not in your mdin
> file it should never be defaulting to 2.0 unless something was very messed
> up in your installation.
> >
> > All the best
> > Ross
> >
> >> On Sep 2, 2015, at 11:51 AM, Lara rajam <lara.4884.gmail.com> wrote:
> >>
> >> Dear Amber !
> >>
> >> I have changed the input as below
> >>
> >> Heating up the system equilibration stage 1
> >>
> >> &cntrl
> >>
> >> nstlim=200000, dt=0.001, ntx=1, irest=0, ntpr=1000, ntwr=1000,
> ntwx=1000,
> >>
> >>
> >> tempi =0.0, temp0=300.0, ntt=1, tautp=2.0,
> >>
> >>
> >> ntb=1, ntp=0,
> >>
> >>
> >> ntc=2, ntf=2,
> >>
> >>
> >> ntr=1,
> >>
> >> /
> >>
> >> Group input for restrained atoms
> >>
> >> 50.0
> >>
> >> RES 1 148
> >>
> >> END
> >>
> >> END
> >>
> >>
> >>
> >> still I get the error !
> >>
> >> the output by default takes the nrespa=2
> >>
> >> as below
> >>
> >>
> >> Heating up the system equilibration stage 1
> >>
> >> &cntrl
> >>
> >> nstlim=100000, dt=0.002, ntx=1, irest=0, ntpr=1000, ntwr=500, ntwx=500,
> >>
> >>
> >> tempi =0.0, temp0=300.0, ntt=1, tautp=2.0,
> >>
> >>
> >> ntb=1, ntp=0,
> >>
> >>
> >> ntc=2, ntf=2,
> >>
> >>
> >> nrespa=2, ntr=1,
> >>
> >> /
> >>
> >> Group input for restrained atoms
> >>
> >> 50.0
> >>
> >> RES 1 148
> >>
> >> END
> >>
> >> END
> >>
> >>
> >>
> >> CUDA (GPU): Implementation does not support nrespa.
> >>
> >> Require nrespa == 1.
> >>
> >>
> >> Input errors occurred. Terminating execution.
> >>
> >>
> >>
> >> still it get killed
> >>
> >>
> >>
> >> On Wed, Sep 2, 2015 at 2:40 PM, David A Case <david.case.rutgers.edu>
> wrote:
> >>
> >>> On Wed, Sep 02, 2015, Lara rajam wrote:
> >>>
> >>>> CUDA (GPU): Implementation does not support nrespa.
> >>>> Require nrespa == 1.
> >>>
> >>> Just leave out any reference to nrespa in your &cntrl namelist.
> >>>
> >>> ...hope this works....dac
> >>>
> >>>
> >>> _______________________________________________
> >>> 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
> >
>
>
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Received on Wed Sep 02 2015 - 15:30:03 PDT
