Dear Prof. Case,
Many thanks for your suggestions.
I ran a short simulation with iwrap =0 with ntpr =1 and what I noticed is
that at 175th step the potential energy value is -5729 kcal/mol and
suddenly shoots to 43796 kcal/mol by the next step.
NSTEP = 175 TIME(PS) = 2506000.363 TEMP(K) = 456.79 PRESS =
0.0
Etot = 4365.3973 EKtot = 10094.7480 *EPtot =
-5729.3507*
BOND = 2780.9813 ANGLE = 2895.3560 DIHED =
265.1213
1-4 NB = 369.9476 1-4 EEL = 875.2511 VDWAALS =
-11459.4185
EELEC = -1456.5895 EHBOND = 0.0000 RESTRAINT =
0.0000
EAMD_BOOST = 0.0000
------------------------------------------------------------------------------
NSTEP = 176 TIME(PS) = 2506000.365 TEMP(K) =********* PRESS =
0.0
Etot = ************** EKtot = ************** * EPtot =
43796.3823*
BOND = 1868.3324 ANGLE = 2993.9430 DIHED =
265.9292
1-4 NB = 522.2288 1-4 EEL = 876.3629 VDWAALS =
38681.8646
EELEC = -1412.2787 EHBOND = 0.0000 RESTRAINT =
0.0000
EAMD_BOOST = 0.0000
------------------------------------------------------------------------------
I am using very low b1 and b2 coefficients (0.10, 0.08) to calculate
accelerated MD parameters. I had even tried creating a bigger boy of CHCl3
with peptide in it and still the same results.
Regarding previous preparation calculations like equilibrium etc were
carried out fine with no abnormal values or results. iwrap=1 option was
used for all steps.
I don't know what are downstream problems.
Please advice as to how can this be solved?
Thank you,
Chetna
On Thu, Nov 15, 2018 at 10:30 PM David Case <david.case.rutgers.edu> wrote:
> On Thu, Nov 15, 2018, Chetna Tyagi wrote:
> >
> >Upon carrying out accelerated MD on a peptide solvated in water and
> >chloroform solvents in *Amber14 pmemd.CUDA.MPI*, I realized that when
> boost
> >to the potential is applied to the Chloroform system, the various values
> in
> >the output result in asterisks....
> >
> >For e.g. NSTEP = 1000 TIME(PS) = 2506002.013 TEMP(K) =*********
> >
> >Based on previous answers, the problem can be traced to high wrapping
> >values which was,
> >
> >*wrapping first mol.: 136974.67863 1318602.52880 -1118357.40723*
> >I used *iwrap =1* option in both cases.
>
> The bad wrapping numbers look more like a downstream problem, caused by
> some earlier problem; but I could be wrong. What happens if you run a
> short simulation (since the problem appears already at step 1000),
> setting iwrap=0? You might also print much more often (i.e. set ntpr=1)
> to get more clues about what might be going wrong.
>
> ....good luck...dac
>
>
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>
--
Best wishes
Chetna
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Received on Fri Nov 16 2018 - 03:00:02 PST
