Hi Vinícius,
Thanks for your advice, but as the same case as of my previous attemps, the
frozen is not succesfull.
I have tried higher values (e.g. 10000.00) without complete frozen. Higher
values causes that the calculation crashes
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.
Thanks in advance
2017-10-27 18:28 GMT+02:00 Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>:
> Hello Danilo,
>
>
> You can use positional restraints for this. In order to do that, add these
> flags into your mdin file:
>
>
> ntr=1, ! Turn on positional restraints
> restraintmask='.CA,C,O,N', ! restraints on the backbone atoms
> only
> restraint_wt=10.0, ! 10.0 kcal/mol.A**2 restraint force constant
>
> Add on your restraintmask flag the name of all atoms you want to restrain
> (on the example I am sending above there are typical names for backbone
> atoms). 10.0 at restraint_wt is a value people generally use during some
> minimizations, thus play with this value until you get the effect you want
> (in your case, higher values).
>
>
> Don't forget to provide a reference structure for the positional
> restraints to pmemd or sander using the flag -ref . In your case, this
> structure would be the initial structure of your simulation.
>
>
> I hope this helps,
>
>
> Vinícius Wilian D Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633
>
> ________________________________
> From: danilo gonzalez <dgnzlzf.gmail.com>
> Sent: Friday, October 27, 2017 12:14:30 PM
> To: amber.ambermd.org
> Subject: [AMBER] frozen atoms.
>
> Hi everyone,
>
> I have some troubles to freeze some atoms during an MD calculation. The
> system contains a protein and a water periodic box. In this calculation, i
> want to freeze the protein residues and let the water residues to
> redistribute.
>
> I it try using the next input:
> Solvent Equilibration
> &cntrl
> imin=0, ntx=5, irest=1,
> ntb=2,cut=8.0,
> ntp=1,
> taup=2,
> ntc=2,
> ntf=2,
> iwrap=1,
> barostat=1,
> ntt=1, temp0=300.0, gamma_ln=0.0,
> nstlim=2500, dt=0.002,
> ntpr=100,ntxo=1,ntwr=100,ntwx=100,ntr=1,ig=19,
> nmropt=1,
> /
> &wt type='TEMP0', istep1=0, istep2=2500,value1=300.0, value2=300.0
> /
> &wt type='END'/
> Protein fixed
> 10.0
> RES 1 464
> END
> END
>
> Increasing the value of the force constant I achieve to reduce the RMSD of
> the system without making it 0.
>
> I've also tried to do the same using the ibelly=1 parameter, but the
> freezing is not successful.
>
> Solvent Equilibration NPT 5 ps
> &cntrl
> imin=0, ntx=5, irest=1,
> ntb=2,cut=8.0,
> ntp=1,
> taup=2,
> ntc=2,
> ntf=2,
> iwrap=1,
> barostat=1,
> ntt=1, temp0=300.0, gamma_ln=0.0,
> nstlim=2500, dt=0.002,
> ntpr=100,ntxo=1,ntwr=100,ntwx=100,ntr=0,ig=19,
> ibelly=1,
> bellymask = ":WAT",
> nmropt=1,
> /
> &wt type='TEMP0', istep1=0, istep2=2500,value1=300.0, value2=300.0
> /
> &wt type='END'
> /
>
> I really appreciate any suggestion.
>
> Thanks in advance.
>
> --
> Danilo González Forero, MSc.
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--
Danilo González Forero, MSc.
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Received on Fri Oct 27 2017 - 12:00:02 PDT
