Dear AMBER Netters,
I am running a molecular dynamics (sander) with a solute solvated with
the CAP option. The CAP option was setup in the topology file, using the
following input file:
PARM98 = loadamberparams /home/serov/local/amber6/dat/parm98.dat
prot = loadPdb prot.pdb
center prot
solvateCap prot WATBOX216 {-19.09, 0.06, -39.98} 37.0
saveAmberParm prot prot_cap.top prot_cap.rst
The input file is the following (no periodic conditions, no GB, no PME):
title
&cntrl
imin=0, ntx=5, ntpr=500,ntwx=500,
ntwe=500, ntcm=1, igb=2, dielc=1,
cut = 14.0, nscm = 1,
ntf=2, ntc=2,
ntb=0, ntp=0,
nstlim=20000,ndfmin=6,nsnb=10,
dt=0.002,
irest=1,
tempi=298.0, temp0=298.0,ntt=1,
ntr=0,
/
The problem is that the temperature of the system is not fixed at 298,
as it should be, but at 306 K:
A V E R A G E S O V E R 25000 S T E P S
NSTEP = 25000 TIME(PS) = 200.000 TEMP(K) = 306.83 PRESS =
.00
Etot = -47666.1630 EKtot = 13078.3885 EPtot =
-60744.5515
BOND = 290.9230 ANGLE = 802.5091 DIHED =
655.1755
1-4 NB = 361.0633 1-4 EEL = 4180.9663 VDWAALS =
8433.4794
EELEC = -75468.6680 EHBOND = .0000 CONSTRAINT =
.0000
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 25000 TIME(PS) = 200.000 TEMP(K) = 1.74 PRESS =
.00
Etot = 4201.3023 EKtot = 73.9777 EPtot =
4200.6323
BOND = 13.7756 ANGLE = 20.4562 DIHED =
17.8306
1-4 NB = 8.6146 1-4 EEL = 23.2842 VDWAALS =
125.9685
EELEC = 4195.5463 EHBOND = .0000 CONSTRAINT =
.0000
------------------------------------------------------------------------------
Do you already have seen such effect ? Is it referenced in the
literature ? Does it come from boundary effect ?
Thank you for your help,
Thérèse Malliavin
Received on Thu Sep 19 2002 - 08:44:24 PDT
