Hi David.
Thanks.
It came out that I had 2 overlapping waters.
Once I have removed it the simulation went as expected.
I am solubilizing a unit cell using addwater program and for some resin
with this protein I am getting this problem with overlapping waters which
are not solved during minimization steps. Now I have to figure out why is
that happening.
Best.
Petro.
On Mon, Jan 6, 2020 at 4:07 PM David Case <david.case.rutgers.edu> wrote:
> 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 Tue Jan 07 2020 - 10:00:02 PST
