<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>Thanks David for the response. I was going through the supporting material of your paper to understand the methodology .</div><div>For G96 forcefield, you wrote</div><div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Times"><span class="Apple-style-span" style="font-size: small;">'For the gromos96 simulations marked “cutoff ” a reaction field with</span><span style="font: 12.0px Helvetica"><span class="Apple-style-span" style="font-size: small;"> </span></span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Times"><span style="font: 12.0px Helvetica"><span class="Apple-style-span" style="font-size: small;">ǫ = 54 </span></span><span class="Apple-style-span" style="font-size: small;">was applied beyond a cutoff of</span><span style="font: 12.0px Helvetica"><span class="Apple-style-span" style="font-size: small;"> 14 </span></span><span class="Apple-style-span" style="font-size: small;">Å, for the opls/aa “cutoff ” simulations a straight cut-off</span><span style="font: 12.0px Helvetica"><span class="Apple-style-span" style="font-size: small;"> </span></span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Times"><span class="Apple-style-span" style="font-size: small;">of</span><span style="font: 12.0px Helvetica"><span class="Apple-style-span" style="font-size: small;"> 14 </span></span><span class="Apple-style-span" style="font-size: small;">Å was chosen, and for the charmm “cutoff ” simulations a shift function was used between</span><span style="font: 12.0px Helvetica"><span class="Apple-style-span" style="font-size: small;"> </span></span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Times"><span class="Apple-style-span" style="font-size: small;">10 and 12 Å. In addition, simulations were carried out using Particle Mesh Ewald (PME) for the</span><span style="font: 12.0px Helvetica"><span class="Apple-style-span" style="font-size: small;"> </span></span></p>
<p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Times"><span class="Apple-style-span" style="font-size: small;">calculation of electrostatic interactions[10, 11].'</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Times"><br class="webkit-block-placeholder"></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Times"><span class="Apple-style-span" style="font-size: medium;">I am wondering what does the statement ' marked cutoff a reaction field with epsilon 54 beyond a cutoff of 14 Angstrom' in terms of gromacs .mdp terminology ? Does it mean that you used reaction field as long range electrostatics for G96. But, I may have understood wrong because in the last line you again write, all simulations used 'PME'.. Does it mean that for G96 , the simulations were repeated with both reaction field and PME separately ?</span></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Times"><font
class="Apple-style-span" size="4"><span class="Apple-style-span" style="font-size: 16px;">For the reaction field, I have never used it before, so I was wondering if you can provide bit more details in 'mdout.mdp' terminolgy for general setup of simulation using G96 forcefield . </span></font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Times"><font class="Apple-style-span" size="4"><span class="Apple-style-span" style="font-size: 16px;">For example, for my simulation using Gromos96, I was using following mdout.mdp using PME. I am not sure that is a suitable setup for gromos simulation or not . Also, if I wanted to use reaction field, what modification I should have made here in long-range electrostat part ?</span></font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Times"><font class="Apple-style-span" size="4"><span class="Apple-style-span" style="font-size: 16px;"><br
class="webkit-block-placeholder"></span></font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Times"><font class="Apple-style-span" size="4"><span class="Apple-style-span" style="font-size: 16px;"><br class="webkit-block-placeholder"></span></font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Times"><font class="Apple-style-span" size="4"><span class="Apple-style-span" style="font-size: 16px;"><br class="webkit-block-placeholder"></span></font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Times"><font class="Apple-style-span" size="4"><span class="Apple-style-span" style="font-size: 16px;"><div>; RUN CONTROL PARAMETERS</div><div>integrator = md</div><div>; Start time and timestep in ps</div><div>tinit = 0.0</div><div>dt = 0.004</div><div>nsteps = 40000000</div><div>; For exact run continuation or redoing
part of a run</div><div>init_step = 0</div><div>; mode for center of mass motion removal</div><div>comm-mode = Linear</div><div>; number of steps for center of mass motion removal</div><div>nstcomm = 1</div><div>; group(s) for center of mass motion removal</div><div>comm-grps =</div><div><div>; NEIGHBORSEARCHING PARAMETERS</div><div>; nblist update frequency</div><div>nstlist = 10</div><div>; ns algorithm (simple or grid)</div><div>ns_type = grid</div><div>; Periodic boundary conditions: xyz (default), no (vacuum)</div><div>; or full (infinite systems only)</div><div>pbc = xyz</div><div>; nblist cut-off</div><div>rlist = 1.4</div><div>domain-decomposition = no</div><div><br class="webkit-block-placeholder"></div><div>; OPTIONS FOR
ELECTROSTATICS AND VDW</div><div>; Method for doing electrostatics</div><div>coulombtype = pme</div><div>rcoulomb-switch = 0</div><div>rcoulomb = 1.4</div><div>; Relative dielectric constant for the medium and the reaction field</div><div>epsilon_r = 1</div><div>epsilon_rf = 1</div><div>; Method for doing Van der Waals</div><div>vdw-type = cut-off</div><div>; cut-off lengths</div><div>;rvdw-switch = 0.7</div><div>rvdw = 1.4</div><div>; Apply long range dispersion corrections for Energy and Pressure</div><div>DispCorr = no</div><div>; Extension of the potential lookup tables beyond the cut-off</div><div>table-extension = 1</div><div>; Seperate tables between energy group pairs</div><div>energygrp_table =</div><div>; Spacing for
the PME/PPPM FFT grid</div><div>fourierspacing = 0.12</div><div>; FFT grid size, when a value is 0 fourierspacing will be used</div><div>fourier_nx = 0</div><div>fourier_ny = 0</div><div>fourier_nz = 0</div><div><div>; EWALD/PME/PPPM parameters</div><div>pme_order = 6</div><div>ewald_rtol = 1e-6</div><div>ewald_geometry = 3d</div><div>epsilon_surface = 0</div><div>optimize_fft = no</div><div><br class="webkit-block-placeholder"></div></div></div></span></font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Times"><br class="webkit-block-placeholder"></p></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><font size="2" face="Tahoma"><hr size="1"><b><span
style="font-weight: bold;">From:</span></b> David van der Spoel <spoel@xray.bmc.uu.se><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Wed, December 22, 2010 2:31:35 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] PME or Reaction field suitable for Gromos forcefield ?<br></font><br>
On 2010-12-22 21.57, Sanku M wrote:<br>><br>><br>> ------------------------------------------------------------------------<br>> *From:* Sanku M <<a ymailto="mailto:msanku65@yahoo.com" href="mailto:msanku65@yahoo.com">msanku65@yahoo.com</a>><br>> *To:* <a ymailto="mailto:gmx-user@gromacs.org" href="mailto:gmx-user@gromacs.org">gmx-user@gromacs.org</a><br>> *Sent:* Wed, December 22, 2010 1:06:09 PM<br>> *Subject:* PME of Reaction field for Gromos forcefield ?<br>><br>> Hi,<br>> I was trying to use g53a5 gromos forcefield for my study of protein in<br>> water . But, I found the original parameterization paper of gromos , in<br>> general uses reaction field for considering long range electrostatics .<br>> But, I was wondering among PME and reaction field , which one will be<br>> more apprpriate . Does PME cause any artifact if used with Gromos<br>> forcefield ?<br>> Alternatively, if I can get a sample
.mdp file for typical gromos<br>> forcefield simulation, that will also be very helpful .<br>> Sanku<br>><br>><br>><br>Check out<br>Oliver Lange, David van der Spoel and Bert de Groot: Scrutinizing <br>Molecular Mechanics Force Fields on the Microsecond Timescale With NMR <br>Data Biophys. J. 99 pp. 647-655 (2010)<br><br>We find that all FF perform better with PME.<br><br><br><br>-- <br>David van der Spoel, Ph.D., Professor of Biology<br>Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br><a ymailto="mailto:spoel@xray.bmc.uu.se" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><span> <a target="_blank" href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a></span><br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><span><a target="_blank"
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