The gmx-developers list is not the forum for these types of questions. I am
replying via gmx-users, which is where the discussion should stay.
I took a few minutes to dig into this. My conclusion is that your system is not
stable. I would encourage you to analyze the temperature and pressure of your
systems that are giving odd results. When I used the topology you provided, the
temperature spiked to over 600 K and the box began to oscillate extensively as
if the system were about to explode. The resulting epsilon value was about 1.6.
If I reduce the timestep to 0.5 fs, the results are much more reasonable, and
using the Ka and Kb values in the paper (not halved!) I get a much more sensible
result, even after just 100 ps. It looks to me as if the combination of these
parameters and a 1-fs timestep is not entirely stable. I know the original
authors used dt = 1 fs, but the point remains.
-Justin
Nilesh Dhumal wrote:
Hello,
I am using flexible water model for my system. I am referring a paper J.
Chem. Phys. 124, 024503 (2006). Author have used Amber type force field.
i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2.
Kbond = 443153.3808 kJ/mol nm**2
Kangle= 317.5656 kJ/mol rad**2.
I am using olss-aa force field parameters in Gromacs VERSION 4.0.7.
I checked some papers in which author have used oplsaa force field in
Gromacs. 1/2 factor is not in opls force field if I compare opls and
amber.
I didn’t get the proper dielectric constant for water when I used the
parameters reported in paper
(Kbond = 443153.3808 kJ/mol nm**2,Kangle= 317.5656 kJ/mol rad**2)
I half the value of Kb and get the proper dielectric constant (~80) for
water reported in paper. If I half Kangle then I don’t get proper
value.
Below are the results for the dielectric constant of water.
Bond length is nm.
Here I have done some analysis. The original value reported in J. Chem.
Phys. 124, 024503 2006, paper are
Kbond = 443153.3808 kJ/mol nm**2
Kangle = 317.5656 kJ/mol rad**2.
bond length Kbond angle Kangle dielectric constant 0.1012
443153.3808 113.24 317.5656 ~1.9 : orginal value
0.1012 221576.6904 113.24 317.5656 ~80 : 1/2 (Kbond)
0.1012 443153.3808 113.24 158.7828 ~1.58 : 1/2 (kangle)
0.1012 221576.6904 113.24 317.5656 ~1.9 : 1/2
(Kbond)&(Kangle)
Here I pasted spc_fw.itp file used for the simulation.
; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
;1 3 yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
opls_1001 OW 8 15.99940 -0.820 A 3.1655e-01 6.503e-01
opls_1002 HW 1 1.00800 0.410 A 0.00e+00 0.00e+00
[ bondtypes ]
; i j func b0 kb
OW HW 1 0.1012 443153.3808 ; J. Chem. Phys.
(2006),124,024503
[ angletypes ]
; i j k func th0 cth
HW OW HW 1 113.24 317.5656 ; J. Chem. Phys.
(2006),124,024503
[ moleculetype ]
; Name nrexcl
WAT 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 opls_1001 1 WAT OW 1 -0.82 15.99940 ;
2 opls_1002 1 WAT HW1 1 0.41 1.008 ;
3 opls_1002 1 WAT HW2 1 0.41 1.008 ;
[ bonds ]
; i j funct
1 2 1
1 3 1
[ angles ]
; i j k funct
2 1 3 1
In water.top file, I included spc_fw.itp file.
; Include water topology
#include "spc_fw.itp"
I run the simulation 6.5 ns for collecting data and I have total 256
water molecules.
Is there anything wrong with my .itp file?
I am using Gromacs VERSION 4.0.7.
Thanks
Nilesh
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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