Dear Prof. Ross,
Thanks for providing insights about the problem. Amber12 in currently
installed on a supercomputing cluster. So, I have to contact the concerned
people in order to modify and recompile amber12.
Thanks,
Mani
On Wed, Jun 25, 2014 at 7:57 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Mani,
>
> The hydrogen mass is hardwired in pmemd.cuda in AMBER 12 so if you are
> modifying it in the prmtop file the sampling will be way off. If you have
> AMBER 14 you should use that since that supports varying masses for
> hydrogen.
>
> If you only have AMBER 12 then first make sure you are fully up to date on
> all patches - the mdout files should be reporting v12.3.1. Then edit
> gputypes.cpp in $AMBERHOME/src/pmemd/src/cuda/ and change line 33 from
> 1.008 to the mass that your hydrogens should be. Then recompile
> pmemd.cuda. (remember that you did this though since it will mess up
> normal calculations).
>
> If you want mixed masses for hydrogen then you will need to update to
> AMBER 14.
>
> Note with masses scaled to half their value it's possible that the system
> won't be stable at 2.0fs. It is probably on the edge of stability as is
> and shake is holding you together. The GPU shake 'may' be less tolerant of
> integration errors than the CPU version so you may still have issues that
> require the timestep to be reduced.
>
> All the best
> Ross
>
>
> On 6/25/14, 2:56 PM, "Manikanthan Bhavaraju"
> <manikanthanbhavaraju.gmail.com> wrote:
>
> >Hi,
> >
> >I am observing sampling issues with pmemd.cuda of Amber12 for a monomer
> >system. Currently, I am using ff9SB forcefield and an explicit solvent
> >model where the masses of solvent and side chains are rescaled by a factor
> >of 0.5. I have tested the performance of pmemd.MPI and pmemd.cuda. The
> >system is stable with pmemd.MPI version. The monomer was minimized and
> >sampled under NVT conditions for 50 ns using the following input files:
> >
> >Minimization step1:
> >
> >&cntrl
> >
> > imin = 1,
> >
> > maxcyc = 5000,
> >
> > ncyc = 2500,
> >
> > ntb = 1,
> >
> > ntr = 1,
> >
> > cut = 12.0,
> >
> > /
> >
> >Hold the protein weakly
> >
> >10.0
> >
> >RES 1 107
> >
> >END
> >
> >END
> >
> >Minimization Step2
> >
> >1REI: initial minimization of the system
> >
> > &cntrl
> >
> > imin = 1,
> >
> > maxcyc = 5000,
> >
> > ncyc = 2500,
> >
> > ntb = 1,
> >
> > ntr = 0,
> >
> > cut = 12.0
> >
> > /
> >
> >Generating initial velocities under NVT conditions:
> >
> >&cntrl
> >
> > imin = 0,
> >
> > irest = 0,
> >
> > ntx = 1,
> >
> > ntb = 1,
> >
> > cut = 12.0,
> >
> > ntr = 1,
> >
> > ntc = 2,
> >
> > ntf = 2,
> >
> > ntt = 3,
> >
> > gamma_ln = 1.0,
> >
> > nstlim = 50000,
> >
> > tempi = 298.15,
> >
> > temp0 = 298.15,
> >
> > dt = 0.002,
> >
> > ntpr = 1000,
> >
> > ntwx = 1000,
> >
> > ntwr = 1000,
> >
> > /
> >
> >keep the protein fixed with weak restraints
> >
> >10.0
> >
> >RES 1 107
> >
> >END
> >
> >END
> >
> >Sampling process:
> >
> >&cntrl
> >
> > imin=0,
> >
> > ntx=5,
> >
> > irest=1,
> >
> > ntc=2,
> >
> > ntf=2,
> >
> > nstlim=5000000,
> >
> > ntt=3,
> >
> > gamma_ln=1.0,
> >
> > temp0=298.15,
> >
> > ntpr=5000,
> >
> > ntwr=5000,
> >
> > ntwx=5000,
> >
> > dt=0.002,
> >
> > ig=-1,
> >
> > ntb=1,
> >
> > cut=12.0,
> >
> > ioutfm=1,
> >
> > /
> >
> >
> >
> >The average RMSd over 50ns was 1.07 +/- 0.01 for the monomer when
> >pmemd.MPI
> >was used. The structures at various intervals were visualized using VMD.
> >The 3D structure of the monomer was retained throughout the simulation.
> >
> >Then, I have used pmemd.cuda in order to run the system for a longer
> >simulation time. The generation of initial velocities and sampling were
> >done using a similar input file that was used for pmemd.MPI. However, the
> >RMSd of the monomer just after 10 ps of the simulation was about 7.0
> >angstrom and keeps increasing all the way to 36.0 angstroms after 10 ns of
> >simulation. The tertiary structure of the monomer was lost and the
> >protein
> >has denatured. So, I have tested the behavior of the system using 1 fs
> >time step. The system was stable until 10 ns of the simulation (RMSd 1.5
> >+/- 0.3). But the extended simulation has once again denatured the
> >protein and the RMSd creeps up quickly.
> >
> >I don't understand why the system is getting destabilized with cuda ? Can
> >someone comment on this issue?
> >
> >Thanks,
> >
> >Mani
> >
> >
> >
> >--
> >Manikanthan Bhavaraju
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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>
--
Manikanthan Bhavaraju
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Received on Wed Jun 25 2014 - 19:00:02 PDT
