Ross,
I gave nscm=0 a try and same result.
NSTEP = 1000 TIME(PS) = 419.000 TEMP(K) = 312.76 PRESS =
0.0
Etot = ************** EKtot = 300.8112 EPtot =
**************
BOND = 80.7068 ANGLE = 182.6906 DIHED =
292.4277
1-4 NB = 85.6465 1-4 EEL = 1165.3455 VDWAALS =
**************
EELEC = ************** EGB = -448.5671 RESTRAINT =
0.0000
Attached are my prmtop and the rst file. This was my input
> CYC MD
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=25000000,dt=0.002,ntb=0,
> tempi=300, temp0=300,
> ntf=2,ntc=2,tol=0.000001,
> ntpr=1000, ntwx=1000, ntwr=1000,
> cut=9999.0, rgbmax=15.0,gbsa=0,
> igb=5,ntt=3,nscm=1000,gamma_ln = 1.0
> /
Thanks
~Levi
On Sat, Apr 24, 2010 at 6:43 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Levi,
>
> > I have been running pmemd.cuda on several different
> > small peptide systems. After minimization and equilibration
> > with sander I run md with pmemd.cuda which produces the
> > following output in the mdinfo file:
> >
> > NSTEP = 1000 TIME(PS) = 419.000 TEMP(K) = 312.76 PRESS =
> > 0.0
> > Etot = ************** EKtot = 300.8112 EPtot =
> > **************
> > BOND = 80.7068 ANGLE = 182.6906 DIHED =
> > 292.4277
> > 1-4 NB = 85.6465 1-4 EEL = 1165.3455 VDWAALS =
> > **************
> > EELEC = ************** EGB = -448.5671 RESTRAINT =
> > 0.0000
>
> > CYC MD
> > &cntrl
> > imin=0,irest=1,ntx=5,
> > nstlim=25000000,dt=0.002,ntb=0,
> > tempi=300, temp0=300,
> > ntf=2,ntc=2,tol=0.000001,
> > ntpr=1000, ntwx=1000, ntwr=1000,
> > cut=9999.0, rgbmax=15.0,gbsa=0,
> > igb=5,ntt=3,nscm=1000,gamma_ln = 1.0
> > /
>
> Can you try this with nscm=0 and see if that works?
>
> Additionally can you send me your input files so I can try this with the
> AMBER 11 code.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
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Received on Sat Apr 24 2010 - 19:30:02 PDT
