AMBER Archive (2003)

Subject: RE: AMBER: constant pressure in GB

From: Yong Duan (yduan_at_udel.edu)
Date: Wed Oct 01 2003 - 20:45:04 CDT

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_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of aini_at_UMDNJ.EDU
> Sent: Wednesday, October 01, 2003 9:19 PM
> To: amber_at_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
>
>
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