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<div class=WordSection1>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span style='font-weight:normal'>Dear gromacs users,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-weight:normal'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-weight:normal'>Does anyone have experience
in implementation of polarizable SWM4-NDP water model by Lamoureux et al. (Chem.Phys.Lett.
418,245 (2006)) in gromacs?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-weight:normal'>I have performed several
simulations with systems of different size (from 1024 up to 8192 water
molecules) with dispersion correction term and the cut-off 15A for both
Ewald and LJ (according to the original paper), but on the regular basis
I have higher density than the one reported in the original paper. Namely, average
molecular volume (calculated by g_energy) is 29.67 (density 1008.25) instead of
29.91 (density 1000.18). Results are same for 4.5.1 and 4.0.7 version
of gromacs. Other parameters such as dielectric constant and surface tension
looks fine, though they have much higher error bars.<o:p></o:p></span></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span style='font-weight:normal'>Below are the .itp
and .mdp files I am using.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-weight:normal'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-weight:normal'>Thank you very much in
advance.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-weight:normal'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-weight:normal'>Mikhail<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-weight:normal'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-weight:normal'>.itp<o:p></o:p></span></p>
<p class=MsoNormal>----------------------------------------------------------------------------------------------------------<o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>[ defaults ]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>; LJ non-bonded Lorenz-Berthelot
Generate 1-4 pairs FudgeLJ FudgeQQ<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'> 1
2
yes
1.0 1.0<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>[ atomtypes ]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>;name
mass charge
ptype c6 c12<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'> WO
15.99940 1.71636e+00 A 0.0 0.0<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'> WH
1.00800 0.55733e+00 A 0.0 0.0<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'> WV 0.0 -1.11466e+00
V 0.0 0.0<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'> WS
0.0 -1.71636e+00 S 0.0 0.0<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>[ nonbond_params ]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>;
sigma
epsilon<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>WO
WO
1
0.318395e+00 882.57296e-03 <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'> [ moleculetype ]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>; molname nrexcl<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>SW4 2<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>[ atoms ]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>; id at type res
nr residu name at name cg
nr charge<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>1 WO 1 SW4 OW1 1
1.71636e+00 <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>2 WH 1 SW4 HW2 1 0.55733e+00<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>3 WH 1 SW4 HW3 1 0.55733e+00<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>4 WV 1 SW4 VW 1
-1.11466e+00<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>5 WS 1 SW4 SW 1
-1.71636e+00<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>[ polarization ]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>; See notes above. alpha (nm^3)<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>1 5 1
0.97825e-03<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>[ settles ]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>; dHH = 0.15139 gives HOH agle equal to 104.52
degree
<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>; i funct dOH dHH<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'> 1 1 0.09572 0.15139<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>;[ constraints ]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>;1 2 1
0.09572<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>;1 3 1
0.09572<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>;3 2 1
0.15139 <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>[ virtual_sites3 ]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>; The position of the virtual site is computed as
follows:<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>; O<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>; <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>; V<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>; <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>; H H<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>; Virtual site from funct a b<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>4 1 2 3 2 0.5 0.024034<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>[ exclusions ]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>; iatom excluded from interaction with i<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>1 2 3 4 5<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>2 1 3 4 5<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>3 1 2 4 5<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>4 1 2 3 5<o:p></o:p></span></p>
<div style='mso-element:para-border-div;border:none;border-bottom:solid windowtext 1.0pt;
padding:0in 0in 1.0pt 0in'>
<p class=MsoNormal style='text-autospace:none;border:none;padding:0in'><span
style='font-size:9.0pt;font-family:"Courier New"'>5 1 2 3 4<o:p></o:p></span></p>
</div>
<p class=MsoNormal><span style='font-weight:normal'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-weight:normal'>.mdp<o:p></o:p></span></p>
<p class=MsoNormal>===================================================================<o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>integrator
= md <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>dt
= 0.001 ;
time step<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>nsteps
= 1000000 ;
number of steps<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>comm_mode =
Linear;Angular ;
Remove center of mass translation and rotation<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>nstcomm
= 1003 ;
reset c.o.m. motion<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>nstxout
= 10000 ;
write coords<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>nstvout
= 10000
; write velocities<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>nstxtcout
=
2000
; write coords to xtc-trajectory file<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>nstlog
= 2000 ;
print to logfile<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>nstlist
= 20 ;
update pairlist<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>ns_type
= grid ;simple ;
pairlist method <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>;================== Polarizable model parameters
=======================<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>emtol
=
0.1
;the convergency criterion for maximum force<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>niter
=
20
;maximum number of iterations for the shell particle optimization<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>;================= Cutt off specification
=============================
<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>pbc
= xyz ;
periodic boundary conditions<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>optimize_fft
= yes ;
perform FFT optimization at start<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>coulombtype
= PME<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>rcoulomb
= 1.5 ;
cut-off for coulomb<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>rlist
= 1.5 ;
cut-off for ns <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>vdw-type
= cut-off<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>rvdw
= 1.5 ;
cut-off for vdw<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>dispcorr
= enerpres<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>;=======================================================================<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>Tcoupl
= v-rescale ; berendsen;nose-hoover; ;
; temperature coupling<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>tc-grps
= SW4 <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>ref_t
= 298.15 <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>tau_t
= 0.1<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>Pcoupl
= berendsen ;
pressure bath<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>Pcoupltype
= isotropic ;
pressure geometry<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>tau_p
= 0.5 ;
p-coupoling time<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>compressibility =
4.5e-5
; <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>ref_p
= 1.01325 <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>;=======================================================================<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>gen_vel
= no ;
generate initial velocities<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>gen_temp
= 300 ;
initial temperature<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:9.0pt;
font-family:"Courier New"'>gen_seed
= 1903 ;
random seed<o:p></o:p></span></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span lang=EN-GB style='font-family:"Arial","sans-serif";
font-weight:normal'>=============================================<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB style='font-family:"Arial","sans-serif";
font-weight:normal'>Dr Mikhail Stukan<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Arial","sans-serif";font-weight:
normal'>Schlumberger Dhahran Carbonate Research Center,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Arial","sans-serif";font-weight:
normal'>Dhahran Techno Valley - KFUPM,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Arial","sans-serif";font-weight:
normal'>P.O. Box 39011, Dammam / Doha Camp 31942,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Arial","sans-serif";font-weight:
normal'>Kingdom of Saudi Arabia</span><span style='font-family:"Arial","sans-serif";
font-weight:normal'><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB style='font-family:"Arial","sans-serif";
font-weight:normal'>Tel: +966 3 331 0300 ext 6182<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB style='font-family:"Arial","sans-serif";
font-weight:normal'>Fax:+966 3 330 0845<br>
<a href="mailto:mstukan@slb.com"><span style='color:blue'>mstukan@slb.com</span></a><o:p></o:p></span></p>
<p class=MsoNormal><o:p> </o:p></p>
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