Hello Justin, I used 0.5 fs time step and still I got dielectric constant ~2.
This is the md.mdp file I used. I checked the temperature it didn't go more than ~ 320 K. title = cpeptide MD cpp = /usr/bin/cpp integrator = md dt = 0.001 ; ps ! nsteps = 6500000 ; total 5 ps. nstcomm = 1000 nstxout = 1000 nstvout = 1000 nstfout = 1 nstlist = 1 ns_type = grid rlist = 0.6 rcoulomb = 0.6 rvdw = 0.7 coulombtype = PME vdwtype = cut-off pbc = xyz fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system ref_t = 295 ; Pressure coupling is on Pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 295.0 gen_seed = 173529 Nilesh On Tue, May 10, 2011 6:14 pm, Justin A. Lemkul wrote: > > 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 didnt 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 dont 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 > > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? 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