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
/\
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|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Sat Apr 24 2010 - 19:00:03 PDT
