Re: AMBER: const-P MD at high T

From: Carlos Simmerling <carlos.ilion.bio.sunysb.edu>
Date: Mon, 18 Oct 2004 12:25:52 -0400

it seems to me that at 600K and 1atm the system is in the gas
phase, so to me this seems like what I would expect. why are
you running at 600K? not to match 600K experiment, so maybe
what you want is to use contant volume at that temperature.
carlos

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================




MURAT CETINKAYA wrote:

>Dear Amber users,
>
>I am trying to run 1ns simulations on my explicitly solvated protein system. But
>when I try to run sander with high system temperatures (more then 500K)sander
>gives out an error saying that:
>
> volume of ucell too big, too many subcells
> list grid memory needs to be reallocated, restart sander
>
>I am also aware that the density continuously falls during the constant pressure
>run. I have performed constant volume runs (prior to const P run)for at least
>100ps (even tried 200ps) but I still get the same result. Here is my input
>file:
>
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 20.0,
> cut = 10, ntr = 0,
> tempi = 600.0, temp0 = 600.0,
> ntt = 1,
> nstlim = 1000000,
> ntpr = 5000, ntwx = 5000, ntwr = 5000
> /
>
>
>Any kind of help really appreciated...
>Thanks,
>
>Murat Cetinkaya
>PennState Univ, UP
>
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Oct 18 2004 - 17:53:00 PDT
Custom Search