Hi Levi,
This is fixed in AMBER 11 now. For your copy try locating the following loop
in cuda/gpu.cpp:
for (int i = gpu->sim.atoms; i < gpu->sim.stride; i++)
{
gpu->pbAtom->_pSysData[i] = 99999999000.0
+ i * 1000.0;
gpu->pbAtom->_pSysData[i + gpu->sim.stride] = 99999999000.0
+ i * 1000.0;
gpu->pbAtom->_pSysData[i + gpu->sim.stride2] = 99999999000.0
+ i * 1000.0;
gpu->pbAtomXYSP->_pSysData[i].x = 99999999000.0f
+ i * 1000.0;
gpu->pbAtomXYSP->_pSysData[i].y = 99999999000.0f
+ i * 1000.0;
gpu->pbAtomZSP->_pSysData[i] = 99999999000.0f
+ i * 1000.0;
}
and change it to:
for (int i = gpu->sim.atoms; i < gpu->sim.stride; i++)
{
gpu->pbAtom->_pSysData[i] = 999999000.0 +
i * 200.0;
gpu->pbAtom->_pSysData[i + gpu->sim.stride] = 999999000.0 +
i * 200.0;
gpu->pbAtom->_pSysData[i + gpu->sim.stride2] = 999999000.0 +
i * 200.0;
gpu->pbAtomXYSP->_pSysData[i].x = 999999000.0f +
i * 200.0;
gpu->pbAtomXYSP->_pSysData[i].y = 999999000.0f +
i * 200.0;
gpu->pbAtomZSP->_pSysData[i] = 999999000.0f +
i * 200.0;
}
See if that works.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Levi Pierce
> Sent: Saturday, April 24, 2010 7:05 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] pmemd.cuda problem
>
> 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.
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Apr 26 2010 - 01:00:03 PDT
