Dear Amber users or developers,
There are two modes (the NAB implementation of nmode is used or the "original" nmode implementation is used.) to calculate entropy in MM_PB/GBSA.
I have used these methods to compute entropy, however, I find there is a huge difference between NAB_nmode and original nmode. So, I want to ask:
First, why arise huge difference between them ? Second, I wang to know which is more accuracy about two modes. Finally, In NAB_nmode,the Amber's
example is as following (input file):
.NM
# Parameters for sander/nmode calculation
# (this section is only relevant if NM = 1 above)
#
# The following parameters are used for entropy calculation using
# gasphase statistical mechanics.
# For further details see documentation.
#
# PROC - Determines which method is used for the calculations:
# By default, PROC = 1, the NAB implementation of nmode is used.
# This allows using either a GB model or a distance-dependent
# dielectric for electrostatic energies. No entropy decomposition
# is possible, however.
# If PROC = 2, the "original" nmode implementation is used.
# Here, only a distance-dependent dielectric is avaliable for
# electrostatic energies. Entropy decomposition is possible
# here, too.
# MAXCYC - Maximum number of cycles of minimization.
# DRMS - Convergence criterion for the energy gradient.
# IGB - Switches between no GB (i.e., vacuum electrostatics) (0) or
# Tsui's GB (1).
# SALTCON - Concentration (in M) of 1-1 mobile counterions in solution.
# EXTDIEL - Dielectricity constant for the solvent.
# SURFTEN - Value used to compute the nonpolar contribution Gnp to
# the desolvation according to Gnp = SURFTEN * SASA.
# DIELC - (Distance-dependent) dielectric constant (if IGB = 0)
#
PROC 1
#
MAXCYC 10000
DRMS 0.5
#
IGB 1
SALTCON 0.00
EXTDIEL 80.0
SURFTEN 0.0072
#
DIELC 4
################################################################################
.PROGRAMS
can you explain the meaning about DIELC - (Distance-dependent) dielectric constant (if IGB = 0)? and why DIELC=4 ? I have test
between DIELC=4 and DIELC=1, and find the result is the same, why?
Appendix
The following is my result about two modes:
NAB_nmode
.NM
PROC 1
#
MAXCYC 10000
DRMS 0.5
#
IGB 1
SALTCON 0.0
EXTDIEL 80
SURFTEN 0.005
DIELC 1
# DELTA
# -----------------------
# MEAN STD
# =======================
TSTRA -14.91 0.00
TSROT -13.92 0.02
TSVIB -0.06 6.53
TSTOT -28.89 6.53
original nmode
.NM
PROC 2
#
MAXCYC 10000
DRMS 0.5
#
IGB 0
SALTCON 0.0
EXTDIEL 80
SURFTEN 0.005
DIELC 4
# DELTA
# -----------------------
# MEAN STD
# =======================
TSTRA -14.91 0.00
TSROT -13.92 0.02
TSVIB -14.68 12.22
TSTOT -43.51 12.22
In order to illustrate the questions in detail, the e-mail is a litte long. Thank you very much.
Sincerely yours
Qiankun Gong
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Received on Fri Aug 17 2018 - 00:30:02 PDT
