On Thu, Mar 08, 2001, kiyean.nam_at_pharma.Novartis.com wrote:
>
>
> Can anyone figure out what went wrong?
>
> Thank you.
>
> Kiyean Nam
>
> molecular dynamics equilibration run using PME
> &cntrl
> imin=0, ntc=2, ntf=2,
> init=3, ntx=1, irest=0,scee=1.2, ntr=0,
> ntb=2, ntp=1, npscal=1, pres0=1.0, taup=0.2,
> nrun=1, nstlim=20000, dt=0.002,
> temp0=300.0, tempI=0.0, ig=71277, ntt=5,
> nmropt=1, iewald=1, ntwx=500,
> &end
> 75.8453196 67.3903038 73.8507727 90.0000000 90.0000000 90.0000000
> 80 72 75 4 0 0 0
> 0.00001
> &wt
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =**********
> Etot = ************ EKtot = 0.0000 EPtot = ************
> BOND = 126.9038 ANGLE = 607.6000 DIHED = 1044.2706
> 1-4 NB = 790.9668 1-4 EEL = 10119.1660 VDWAALS = ************
> EELEC = -178932.6354 EHBOND = 0.0000 CONSTRAINT = 0.0000
> EKCMT = 0.0000 VIRIAL = ************ VOLUME = 377468.9592
> T_SOLUTE = 0.0000 T_SOLVENT = 0.0000
> Density = 0.9774
You are trying to run a constant pressure simulation before equilibrating
the system to room temperature. You have to get the system heated up first
before trying to adjust the volume by setting ntp>0.
However, it also looks like something is wrong with your "minimized"
structure, since the van der Waals energy is all stars....you most likely
have atoms (nearly) on top of each other. Study very carefully the
output from the minimization, and make sure that step "0" of the MD
matches in energy the final step from the minimization. (I'm assuming
that you used PME for the minimzation as well.)
...good luck....dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Thu Mar 08 2001 - 09:28:28 PST
