AMBER Archive (2008)

Subject: Re: AMBER: Q: ntc = 3 parallel runnable not compiled in Amber 9?

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Jul 31 2008 - 07:07:21 CDT

it's because of shake. you can calculate and energy but not do MD steps.
this is a limitation in the code and can't be changing through compiler options.
I think most people use only ntc=2, not 3. is there a reason you must constrain
all bonds?

On Wed, Jul 30, 2008 at 11:51 PM, Qicun Shi <qshi01_at_gmail.com> wrote:
> Dear Dr Case or Other Amber Users:
>
> This is Qicun Shi at University of Notre Dame. I have used Amber 9.0
> for sometime and recently I was trying to run with Langevin dynamics,
> but my job showed to me the following message,
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 148.61 PRESS =
> -5522.2
> Etot = -154846.3195 EKtot = 10723.6486 EPtot =
> -165569.9681
> BOND = 0.0000 ANGLE = 542.8270 DIHED =
> 1269.8744
> 1-4 NB = 505.1394 1-4 EEL = -15112.3067 VDWAALS =
> 27646.0326
> EELEC = -180493.0302 EHBOND = 0.0000 RESTRAINT =
> 71.4955
> EAMBER (non-restraint) = -165641.4636
> EKCMT = 3145.4111 VIRIAL = 56862.3861 VOLUME =
> 450529.0504
> Density =
> 0.8011
> Ewald error estimate: 0.2584E-03
> SGFT= 0.0000 TEMPSGI= 1.0000 K
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 71.496 Angle = 0.000 Torsion = 0.000
> ===============================================================================
> this parallel version only works for ntc < 3
> only fast water and bonds with H.
>
> Could you show me if this error is due to parallel compiling or other
> reasons? If it is from compiling, how to re-compile the parallel
> for ntc =3? I was puzzling that why sander.MPI runs at step 0
> while giving energy information. If the error is right, then it should
> never run.
>
> Thanks in advance for help.
>
> Qicun 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
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Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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