<p style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 10pt; mso-layout-grid-align: none" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">Hi all.</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; TEXT-INDENT: 35.4pt; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">I have to reproduce an experiment from the article "Identification of the nucleophilic factors and the productive complex for the editing reaction by leucyl-tRNA synthetase" (by Yohsuke Hagiwara a,b, Osamu Nureki c, Masaru Tateno a,b,*). This is one of the steps of education I have to complete. All actions described in this article were made with Amber9. I'm a newer in modelling and I have only gromacs tools (v4.0.4), so <span style="COLOR: black">I have downloaded amber force field port-files (</span></span><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US; mso-fareast-font-family: TimesNewRomanPSMT" lang="EN-US">E.J. Sorin, S. Park</span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">).</span><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US"> I want to know whether my mdp files are reflexing the data I need. So this is a chapter from article:</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; TEXT-INDENT: 35.4pt; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US"> </span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; TEXT-INDENT: 35.4pt; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">"…1. <span style="COLOR: black">MD simulations were performed using the AMBER 9 program. The parm99 force field was applied to the atoms of LeuRS and tRNALeu, and the TIP3P model was used for the solvent water molecules. Electrostatic interactions were calculated by the particle-mesh Ewald (PME) method, using 1.0 as the dielectric constant. A cut-off of 12 </span></span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt">å</span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US"> was used to calculate the direct space sum for PME; the electrostatic interactions beyond 12 </span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt">å</span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US"> were calculated in reciprocal space by the fast Fourier transform method.</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">Thus, all electrostatic interactions between atoms were calculated. The SHAKE algorithm was used to restrain the bond lengths involving hydrogen atoms. The time step for integration was set to 1 fs. The temperature and pres-sure were set using the Berendsen algorithm.</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; TEXT-INDENT: 35.4pt; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">The initial coordinates used for the present MD simulations were from the modelled structure previously constructed for LeuRS complexed with valyl-tRNALeu. For the present system, we immersed the complex in a solvent box comprising 49 587 water molecules, and used the periodic boundary condition where the size of the unit box was 103.0 _ 138.3 _ 117.1 </span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt">å</span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">3. The total number of atoms in the system was 165 739. In the initial (relaxation) phase of the MD simulation, the water molecules were relaxed at 300 K for 10 ps, while the atoms of the protein and tRNALeu were positionally constrained by a harmonic function using a force constant of 500 kcal/mol </span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt">å</span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">2. The force constant was then reduced to 250, 125, 50, 25, 10, and 5 kcal/mol </span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt">å</span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">2 in six MD simulations. The time consumed by each simulation was 2 ps…(then free MD)…</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; TEXT-INDENT: 35.4pt; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">2. This equilibrated system was used for further structural modeling to investigate the hydrated structure relevant to the editing reaction, in which 1 ns MD simulations were performed in the presence of constraints to effectively explore the states. First, with respect to the atomic distance between the carbonyl carbon of the substrate and the oxygen atom of the identified nucleophilic water, a constrained MD simulation was performed to investigate the</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">mechanisms of the approach of the water molecule. This simulation was started by using a harmonic potential as the distance constraint, where the force constant was set to 5 kcal/mol </span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt">å</span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">2. When the atomic distance was not reduced any further, despite the presence of the harmonic potential in the MD simulation (at about 470 ps), the force constant was increased up to 200 kcal/mol </span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt">å</span><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">2; this was exploited to mimic the first phase of a nucleophilic attack in the MD simulations, which enabled us to explore larger conformational spaces than with the first principles MD simulations. A similar protocol was applied in other constrained MD simulations for efficient explorations of conformational spaces. To obtain a PMF with respect to the rotation of the dihedral angle, C40–C30–O30–HO30 , we employed the umbrella sampling technique, using 14 windows in the range of 50–180_. Umbrella sampling is a theoretical technique to efficiently search for not only energetically favourable but also energetically-unfavourable conformations in a phase space of a system, combined with a bias potential (e.g. a harmonic potential) to overcome energy barriers. The force constants of the<span style="mso-spacerun: yes"> </span>potential in those windows were set to 10.0 kcal/mol rad2.</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; TEXT-INDENT: 35.4pt; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">The structures obtained using MD simulations were evaluated by exploiting quantum mechanics/molecular mechanics (QM/MM) hybrid calculations in terms of the stability and reactivity. For this purpose, our interface program was used to connect QM (gamess) andMM(amber) engines..."</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US"> </span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">Questions:</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">1.First of all, can I use spc instead op tip3p? Some problems occured when I tried to full the genbox with water… not enough memory (it’s not true, I made my box corresponding to the values mentioned above).</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US"> </span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; COLOR: black; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">2.</span><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US"> First part of MD (1.)</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">cpp<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>/lib/cpp -traditional ;</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">define<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>-DFLEXIBLE;</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">constraints<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>hbonds</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">constraint_algorithm =<span style="mso-spacerun: yes"> </span>SHAKE</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">integrator<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>md</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">dt<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>0.001</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">nsteps<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>20000</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">nstxout<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>2000</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">nstxtcout<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>2000</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">nstvout<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>2000</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">nstfout<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>2000</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">nstlog<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>2000</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">coulombtype<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>PME</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">rcoulomb<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>1.0</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">rcoulomb_switch<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>0</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">pme_order<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>4</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">optimize_fft<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>yes</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">fourierspacing<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>0.12</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">ns_type<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>grid</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">vdwtype<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>Cut-off</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">rlist<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>1.0</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">rvdw<span style="mso-spacerun: yes"> </span><span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>1.4</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">nstlist<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>10</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">; Generate velocites is on at 300 K.</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">gen_vel<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>yes</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">gen_temp<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>300</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">gen_seed<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>173529</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">; Berendsen temperature coupling is on in four groups</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">Tcoupl<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>v-rescale</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">tau_t<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>0.1<span style="mso-spacerun: yes"> </span>0.1<span style="mso-spacerun: yes"> </span></span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">tc_grps<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>protein<span style="mso-spacerun: yes"> </span>non-protein</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">ref_t<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>300<span style="mso-spacerun: yes"> </span>300<span style="mso-spacerun: yes"> </span></span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">; Pressure coupling </span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">Pcoupl<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>berendsen</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">tau_p<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>0.5</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">pcoupltype<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>isotropic</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">compressibility<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>13.5e-5</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">ref_p<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>3.0</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">; COM PULLING<span style="mso-spacerun: yes"> </span></span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">; Pull type: no, umbrella, constraint or constant_force</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">pull<span style="mso-spacerun: yes"> </span>= umbrella</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">pull_geometry<span style="mso-spacerun: yes"> </span>= position</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">pull_dim<span style="mso-spacerun: yes"> </span>= Y Y Y</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">pull_group0<span style="mso-spacerun: yes"> </span>= protein</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">pull_group1<span style="mso-spacerun: yes"> </span>= non-protein</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">pull_vec1<span style="mso-spacerun: yes"> </span>= 0.0 0.0 0.0</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">pull_init1<span style="mso-spacerun: yes"> </span>= 0.0 0.0 0.0</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">pull_rate1<span style="mso-spacerun: yes"> </span>= 0.0</span></p>
<p style="TEXT-ALIGN: justify; LINE-HEIGHT: normal; MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class="MsoNormal"><span style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">pull_k1<span style="mso-spacerun: yes"> </span>= 2093</span></p>
<p style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US"> </span></p>
<p style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">(In each of the six following simulations I will change just a number of steps and pull value)</span></p>
<p style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">3. How can I perform a second part of simulation with a distance pull on carbonyl carbon and water molecule? I have to rename this water and atom as separate molecule? Any ideas?</span></p>
<p style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US"> And the last one...for what reason they used this force in pulling, not another?</span></p>
<p style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 10pt" class="MsoNormal"><span style="LINE-HEIGHT: 115%; FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 10pt; mso-ansi-language: EN-US" lang="EN-US">Thank you, yours faithfully.</span></p>