AMBER Archive (2004)

Subject: Re: AMBER: MD run: frozen

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Sun Nov 28 2004 - 09:32:25 CST

do I understand correctly that you solvated the system with explicit
solvent,
and then used GB solvation as well? that is probably not what you want to
do.

is there anyone there that has experience with MD simulations? you might
want to sit down with that person and discuss your inputs before you try
them.

bybaker_at_itsa.ucsf.edu wrote:

>Hello, Amber:
>
>I am running MD simulation on my protein model with implicit solvent. The
>protein was solvated with WATBOX 216. The system had been minimized by
>1000 steps. When I try to heat up the system before the production MD
>run, it was freezed. I use Amber7.
>
>Here is my input:
>
>----
>Initial molecular dynamic, heating up the system, implicit solvent, eq-1:
>
> &cntrl
> imin=0, irest =0, ntx =1,
> ntt=1, tempi=0.0, temp0=310,o, tautp=2, ig=209858,
> ntp=0, igb=1,
> ntb=0, ntc=2, ntf=2,
> nstlim=5000, ntwx=5000, ntpr=500,
> &end
>
>-----
>
>Here is where it was frozen from the output:
>
>----
>
>4. RESULTS
>
>NSTEP=0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
>Etot = -100275.7996 EKtot = 0.0000 EPtot = -100275.7996
>BOND = 100.0539 ANGLE = 439.6208 DIHED = 1171.2667
>1-4 NB = 651.1748 1-4 EEL = 9036.3355 VDWAALS = -2744.5899
>EELEC = -86130.8493 EGB = -22798.8122 RESTRAINT = 0.0000
>
>-----
>No more output after one hour.
>
>Can anyone give me some suggestions on how to fix the probelm?
>
>Thank you for your help.
>
>Bo
>
>
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