On Mon, Jan 06, 2020, Petro wrote:
>I am getting this problem while simulating a protein crystal.
>Minimization looks fine, but once I start MD simulation proteins are
>getting wrapped out from the cell on some huge distances. I am running it
>using pmemd.cuda.
>--------------------------------------------------------------------------------
> 4. RESULTS
>--------------------------------------------------------------------------------
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 199.47 PRESS =
>0.0
> Etot = -25764.3069 EKtot = 10965.6607 EPtot =
> -36729.9676
> BOND = 1130.2278 ANGLE = 1850.5557 DIHED =
>10024.1760
> 1-4 NB = 3278.5132 1-4 EEL = 41285.7243 VDWAALS =
>-9056.7026
> EELEC = -85242.4620 EHBOND = 0.0000 RESTRAINT =
>0.0000
> ------------------------------------------------------------------------------
>
>wrapping first mol.:*************** 15762562.76400 14220054.31873
Your calculation is probably failing long before it gets to the stage
of wrapping. Run a short (say 100 step) simulation with ntpr=1. That
will provide a lot more information on what is happening.
You can also compare the short simulation with one that is run on the
CPU: for certain types of problems, one gets better error messages from
the CPU version.
....dac
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Received on Mon Jan 06 2020 - 07:30:03 PST
