In GB simulation, solvent is represented by an analytical function such
that it is intended to mimic infinitely dilute system. At the present,
pressure is not calculated and is not controlled.
yong
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of aini.UMDNJ.EDU
> Sent: Wednesday, October 01, 2003 9:19 PM
> To: amber.scripps.edu
> Subject: AMBER: constant pressure in GB
>
>
> Hello,
>
> Is it possible to have constant pressure (e.g. 1 atm) in GB
> simulation? I have
> minimized the protein-ligand complex. In the equilibration,
> the system was
> heated up to 300K. In output file:
>
> NSTEP = 3450 TIME(PS) = 6.900 TEMP(K) = 292.00
> PRESS = 0.0
> Etot = -3476.7635 EKtot = 3804.4867 EPtot =
> -7281.2502
> BOND = 937.6709 ANGLE = 2315.2862 DIHED =
> 3282.1783
> 1-4 NB = 1326.5105 1-4 EEL = 13682.1958 VDWAALS =
> -2482.9081
> EELEC = -21886.4208 EGB = -5767.0078 RESTRAINT =
> 1235.6113
> ESURF = 75.6335
> EAMBER (non-restraint) = -8516.8615
>
> It looks like the pressure in my system is 0 atm. I think it's wrong.
>
> Here is my input file for equlibration.
>
> &cntrl
> imin = 0,
> ntc = 2, ntf = 2,
> cut = 12.0, igb = 2, saltcon = 0.002, gbsa = 1,
> ntpr = 50,
> nstlim = 10000, dt = 0.002,
> ntt = 1, tempi = 100.0, temp0 = 300, taup = 1.0,
> ntx = 1, irest = 0, ntb = 0,
> nscm = 1000,
> ntr = 1,
> &end
> keep all atom frozen
> 5
> RES 1 328
> END
> END
>
>
> What might be the problem?
> Thanks in advance.
>
> aini
>
>
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Oct 02 2003 - 02:53:00 PDT
