<p align="center"> </p>
<p><span lang="EN-US"><font size="3" face="Times New Roman">Dear all,</font></span></p>
<p><span lang="EN-US"><font size="3" face="Times New Roman">I’m working on some simulations about the adsorption of protein on solid surfaces, which have<span style="color: blue; mso-bidi-font-weight: bold"> slab geometry in the x-y plane</span>. In order to reduce the amount of water molecules and at the same time to <span style="color: blue">decrease the unphysical Coulomb interaction between periodic images in the z-direction</span>, an empty layer should be added in the z-direction. To prevent the water molecules from evaporating into the vacuum layer, I’m going to use the <b>wall </b>option. However, there are some details that I’m not sure about.</font></span></p>
<p><span lang="EN-US"><font face="Times New Roman"><font size="3">What are your suggestions about the choice of <b><i>wall_atomtype</i></b> and <b><i>wall_type</i></b></font></font><a name="OLE_LINK2" target="_blank"><font size="3" face="Times New Roman">?</font></a><font size="3" face="Times New Roman"> Is it necessary to leave some room for the two walls (or it may lead to high interaction energies between the walls and the system) and how to determine its height (in my simulations, <span style="color: #c00000">I leave about 1.5 Å, respectively</span>)? Does it have something to do with the <b><i>wall_atomtype</i></b> and <b><i>wall_type</i></b>?</font></span></p>
<p><span lang="EN-US"><font size="3" face="Times New Roman">When choose <b><i>nwall=2</i></b>, pressure coupling and Ewald summation can be used (<span style="color: blue">it is usually best to use semi-isotropic pressure coupling with x/y compressibility set to 0</span>). It means the wall can move in the z-direction? Can the pressure coupling be used in system with fixed atoms and how can we control/calculate the pressure of the mobile phase (as it has been discussed in the paper [</font><a href="http://link.springer.com/article/10.1116/1.3493470" target="_blank"><font size="3" face="Times New Roman">Biointerphases <b>5</b>, 85 (2010)</font></a><font size="3" face="Times New Roman">] using the CHARMM package)? </font></span></p>
<p><font face="Times New Roman"><font size="3"><span lang="EN-US" style="mso-bidi-font-weight: bold">When combing walls with the PME method, it is suggested the<b><i> eward_geometry</i></b> be set to <b><i>3dc </i></b>and the <b><i>wall_eward_zfac</i></b> be <b><i>3</i></b>. Does this mean there will be an empty layer </span><span lang="EN-US" style="color: blue">whose height is 3 times the slab height </span><span lang="EN-US" style="mso-bidi-font-weight: bold">added to increase the z-dimension of the box? And I’m not sure about the exact meaning of the “slab height”; it seems to be the length/width of the slab (as described in the paper [<a href="http://jcp.aip.org/resource/1/jcpsa6/v111/i7/p3155_s1" target="_blank">J. Chem. Phys. <b>111</b>, 3155 (1999)</a>]).</span></font></font></p>
<p><span lang="EN-US"><font size="3" face="Times New Roman">I’m so sorry for troubling you with so many questions. But I need your help badly and sincerely. Anyone can help me? Thank you!!</font></span></p>
<p><span lang="EN-US"><font size="3" face="Times New Roman">Bellow is an attachment of mdp file used in my simulation work. If there is anything wrong, please be kind to point it out. Thanks again!</font></span></p>
<p><span lang="EN-US"><font face="Times New Roman"><font size="3">Chunwang Peng</font></font></span></p>
<p><font size="3"><span lang="EN-US"><font face="Times New Roman">Room 302, Building 16</font></span><span style="font-family: ËÎÌå; mso-ascii-font-family: 'Times New Roman'; mso-hansi-font-family: 'Times New Roman'">£¬</span><span lang="EN-US"></span></font></p>
<p><font size="3"><span lang="EN-US"><font face="Times New Roman">Chemistry & Chemical Engineering</font></span><span style="font-family: ËÎÌå; mso-ascii-font-family: 'Times New Roman'; mso-hansi-font-family: 'Times New Roman'">£¬</span><span lang="EN-US"></span></font></p>
<p><font size="3"><span lang="EN-US"><font face="Times New Roman">South China University of Technology</font></span><span style="font-family: ËÎÌå; mso-ascii-font-family: 'Times New Roman'; mso-hansi-font-family: 'Times New Roman'">£¬</span><span lang="EN-US"></span></font></p>
<p><span lang="EN-US"><font size="3" face="Times New Roman">Tianhe District, Guangzhou </font></span></p>
<p><span lang="EN-US"><font size="3" face="Times New Roman"> </font></span></p>
<p><span lang="EN-US"><font size="3" face="Times New Roman">md.mdp</font></span></p>
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<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">title<span style="mso-tab-count: 2"> </span>= cyt-c on Au MD </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; Run parameters</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">integrator<span style="mso-tab-count: 1"> </span>= md<span style="mso-tab-count: 2"> </span>; leap-frog integrator</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">nsteps<span style="mso-tab-count: 2"> </span>= 10000000<span style="mso-tab-count: 1"> </span>; 2 * 10000000 = 20000 ps, 20 ns</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">dt<span style="mso-tab-count: 2"> </span>= 0.002<span style="mso-tab-count: 2"> </span>; 2 fs</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">comm-mode<span style="mso-spacerun: yes"> </span>= Linear<span style="mso-spacerun: yes"> </span>; mode for center of mass motion removal</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt"> </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; Output control</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">nstxout<span style="mso-tab-count: 2"> </span>= 10000<span style="mso-tab-count: 2"> </span>; save coordinates every 20 ps</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">nstvout<span style="mso-tab-count: 2"> </span>= 10000<span style="mso-tab-count: 1"> </span><span style="mso-tab-count: 1"> </span>; save velocities every 20 ps</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">nstenergy<span style="mso-tab-count: 1"> </span>= 10000<span style="mso-tab-count: 2"> </span>; save energies every 20 ps</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">nstlog<span style="mso-tab-count: 2"> </span>= 10000<span style="mso-tab-count: 2"> </span>; update log file every 20 ps</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt"> </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; Selection of energy groups</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">energygrps<span style="mso-spacerun: yes"> </span>= Protein_HEM<span style="mso-spacerun: yes"> </span>GLD ;Group(s) to write to energy file</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt"> </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; Bond parameters</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">continuation<span style="mso-tab-count: 1"> </span>= yes<span style="mso-tab-count: 2"> </span>; Restarting after NPT </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">constraint_algorithm = lincs<span style="mso-tab-count: 1"> </span>; holonomic constraints, GolP has been tested with lincs only </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">constraints<span style="mso-tab-count: 1"> </span>= hbonds<span style="mso-tab-count: 1"> </span>; bonds with H-atoms constrained</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">lincs_iter<span style="mso-tab-count: 1"> </span>= 1<span style="mso-tab-count: 2"> </span>; accuracy of LINCS</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">lincs_order<span style="mso-tab-count: 1"> </span>= 4<span style="mso-tab-count: 2"> </span>; also related to accuracy</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt"> </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; Neighborsearching</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">ns_type<span style="mso-tab-count: 2"> </span>= grid<span style="mso-tab-count: 2"> </span>; search neighboring grid cells</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">nstlist<span style="mso-tab-count: 2"> </span>= 10<span style="mso-tab-count: 2"> </span>; 20 fs</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">rlist<span style="mso-tab-count: 2"> </span>= 1.1<span style="mso-tab-count: 2"> </span>; short-range neighborlist cutoff (in nm)</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; Periodic boundary conditions</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">pbc<span style="mso-tab-count: 2"> </span>= xy<span style="mso-tab-count: 2"> </span>; 2-D PBC</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt"> </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; Method for doing Van der Waals</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">vdw-type<span style="mso-spacerun: yes"> </span>= switch</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">rvdw-switch<span style="mso-spacerun: yes"> </span>= 0.9</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">rvdw<span style="mso-tab-count: 2"> </span>= 1.0<span style="mso-tab-count: 2"> </span>; short-range van der Waals cutoff (in nm)</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt"> </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; Electrostatics</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">coulombtype<span style="mso-tab-count: 1"> </span>= PME<span style="mso-tab-count: 2"> </span>; Particle Mesh Ewald for long-range electrostatics</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">rcoulomb<span style="mso-tab-count: 1"> </span>= 1.1<span style="mso-tab-count: 2"> </span>; short-range electrostatic cutoff (in nm)</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">pme_order<span style="mso-tab-count: 1"> </span>= 4<span style="mso-tab-count: 2"> </span>; cubic interpolation</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">fourierspacing<span style="mso-tab-count: 1"> </span>= 0.12<span style="mso-tab-count: 2"> </span>; grid spacing for FFT</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">ewald_rtol<span style="mso-spacerun: yes"> </span>= 1e-5</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">ewald_geometry<span style="mso-spacerun: yes"> </span>= 3dc</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt"> </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; FFT grid size, when a value is 0 fourierspacing will be used</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">fourier_nx<span style="mso-spacerun: yes"> </span>= 0</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">fourier_ny<span style="mso-spacerun: yes"> </span>= 0</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">fourier_nz<span style="mso-spacerun: yes"> </span>= 0</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">optimize_fft<span style="mso-spacerun: yes"> </span>= yes</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt"> </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; Temperature coupling is on</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">tcoupl<span style="mso-tab-count: 2"> </span>= Nose-Hoover<span style="mso-tab-count: 2"> </span>; Nose-Hoover thermostat</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">tc-grps<span style="mso-tab-count: 1"> </span>= Protein_HEM GLD<span style="mso-tab-count: 1"> </span>Water_and_ions<span style="mso-spacerun: yes"> </span>; three coupling groups - more accurate</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">tau_t<span style="mso-tab-count: 2"> </span>= 0.5<span style="mso-tab-count: 1"> </span>0.5<span style="mso-tab-count: 1"> </span>0.5<span style="mso-tab-count: 1"> </span>; time constant, in ps</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">ref_t<span style="mso-tab-count: 2"> </span>= 300 300 <span style="mso-tab-count: 1"> </span>300<span style="mso-tab-count: 1"> </span>; reference temperature, one for each group, in K</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt"> </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; Pressure coupling is on</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">pcoupl<span style="mso-tab-count: 2"> </span>= Parrinello-Rahman<span style="mso-tab-count: 1"> </span>; Pressure coupling on in NPT</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">pcoupltype<span style="mso-tab-count: 1"> </span>= semiisotropic<span style="mso-tab-count: 1"> </span>; nonuniform scaling of box vectors</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">tau_p<span style="mso-tab-count: 2"> </span>= 1.0<span style="mso-tab-count: 1"> </span>1.0<span style="mso-tab-count: 2"> </span>; time constant, in ps</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">ref_p<span style="mso-tab-count: 2"> </span>= 1.0<span style="mso-tab-count: 1"> </span>1.0<span style="mso-tab-count: 2"> </span>; reference pressure, in bar</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">compressibility = 0<span style="mso-tab-count: 1"> </span>4.5e-5<span style="mso-tab-count: 2"> </span>; isothermal compressibility of water, bar^-1</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt"> </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; Velocity generation</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">gen_vel<span style="mso-tab-count: 2"> </span>= no<span style="mso-tab-count: 2"> </span>; Velocity generation is off </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt"> </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; Non-equilibrium MD stuff</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">freezegrps<span style="mso-spacerun: yes"> </span>= LOCK</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">freezedim<span style="mso-spacerun: yes"> </span>= Y<span style="mso-spacerun: yes"> </span>Y<span style="mso-spacerun: yes"> </span>Y</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt"> </span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; WALLS<span style="mso-spacerun: yes"> </span><span style="mso-spacerun: yes"> </span></span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">; Number of walls, type, atom types, densities and box-z scale factor for Ewald</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">nwall<span style="mso-spacerun: yes"> </span>= 2</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">wall_type<span style="mso-spacerun: yes"> </span>= 9-3</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">wall_r_linpot<span style="mso-spacerun: yes"> </span>= -1<span style="mso-spacerun: yes"> </span>-1</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">wall_atomtype<span style="mso-spacerun: yes"> </span>= OWT3<span style="mso-spacerun: yes"> </span>OWT3<span style="mso-spacerun: yes"> </span>; oxygen of TIP3P water in charmm27.ff</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">wall_density<span style="mso-spacerun: yes"> </span>= 33.4<span style="mso-spacerun: yes"> </span>33.4</span></p>
<p align="left"><span lang="EN-US" style="font-family: 'Courier New'; font-size: 9pt; mso-font-kerning: 0pt">wall_ewald_zfac<span style="mso-spacerun: yes"> </span>= 3</span></p>
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