I am really sorry. I should have posted the output. Here is the output.
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 299.88 PRESS =
0.0
Etot = ************** EKtot = 4923882.0151 EPtot =
**************
BOND = 1853006.2443 ANGLE = 168361.5165 DIHED =
311333.5535
1-4 NB = ************** 1-4 EEL = 972862.9311 VDWAALS =
**************
EELEC = -19214245.2191 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
59839703.9396
Density =
0.9374
regards
Tanmoy
On Sun, Nov 6, 2022 at 5:00 PM David A Case <david.case.rutgers.edu> wrote:
> On Sun, Nov 06, 2022, Tanmoy Paul via AMBER wrote:
>
> > It did not work. The error remains the same. Any other tips?
>
> This is not very helpful. What is "it" that did not work? What did you
> change? What is the "error" that remains the same? Did you run a
> zero-step
> MD run, as suggested?
>
> ...thx...dac
>
> >>> Let's try to narrow down the problem: as an experiment, try a much
> smaller
> >>> buffer, say 8 Ang. instead of 12. This will lead to many fewer
> atoms. Do
> >>> you still see problems? If you do, leave out the water altogether --
> >>> let's see if the protein system itself is leading to problems.
> >>>
> >>> Loading a prmtop file from Amber16 into VMD might not be the best way
> to
> >>> tell if there are problems. Try running a zero-step MD (nstlim=0), and
> >>> see if you get reasonable energies, especially (say) for the bonded
> terms.
>
>
>
--
With regards,
Tanmoy
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Received on Sun Nov 06 2022 - 16:30:02 PST
