Hii;
May be I am not suitable to answer you more precisely but looks like you
have a tempo and tempi problem. See when you are running heating step your
input and output is same the input and output temperature is 298.15 K why
not you put a tempi=0K and tempi=300k and after that heating stage put a
equilibration stage using at 300K NPT (ntb=2,ntp=1,ntt=3,gamma_ln=1.0)
ensemble before production run NVT (ntb=1,ntp=0,ntt=1,tautp=10.0) ensemble.
Then draw RMSD profile using CPPTRAJ check the box size and duplicated this
process with pmemd.mpi. Put sanapshots in the production run using CPPTRAJ
from pmemd.MPI and pmemd.cuda and compare against strating structure. See
whats there.
Best!!
SB
On Thu, Jun 26, 2014 at 3:26 AM, 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
>
--
Thanks & Regards;
Soumendranath Bhakat
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 25 2014 - 15:30:02 PDT
