Dear gromacs users,<br><br>Recently I stumbled over following paper:<br>T. Terakawa, T. Kameda, and S. Takada, On Easy Implementation of a Variant of the Replica Exchange with Solute Tempering in GROMACS. Journal of Computational Chemistry 32 (2011) 1228-1234.<br>
<br>The authors suggested an easy way to run this kind of simulation with Gromacs, without even changing the code. The only thing that is need, is the the rescaling of the parameters in the parameter file. Since the reduction of the replica number is quite appealing to me I wonder which file I have to change? Actually, I thought of manipulating the .tpr file or to rescale and creating the force fields for every replicate. Is this feasible, or is there a better way?<br>
<br>Manipulating the .tpr file could be easier, since it unifies (right?) the parameters from the different force fields, before sending it to the mdrun application. But for this I would like to understand the tpr file first.There are quite a lot of entries and first I try to understand LJ interactions and how they are defined in this file. I found two entries<br>
<br>LJ14<br> functype[154]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00<br> functype[155]=LJ14, c6A= 4.46680887e-03, c12A= 4.74702711e-06, c6B= 4.46680887e-03, c12B= 4.74702711e-06<br>
<br>which corresponds to following interactions <br><br> LJ-14:<br> nr: 876<br> iatoms:<br> 0 type=154 (LJ14) 0 4<br> 1 type=155 (LJ14) 0 5<br><br>When I tried to calculate the parameters from the combination rules (in this case Gromos 53A6 force field), I found (the highlighted columns contain the original parameters for the specific atom groups from the Gromos documentation and the calculated value for combining the two parameters:<br>
<table style="border-collapse: collapse; width: 621pt;" border="0" cellpadding="0" cellspacing="0" width="825"><col style="width: 114pt;" width="152">
<col style="width: 44pt;" span="3" width="58">
<col style="width: 91pt;" width="121">
<col style="width: 85pt;" width="113">
<col style="width: 89pt;" width="119">
<col style="width: 110pt;" width="146">
<tbody><tr style="height: 15pt;" height="20">
<td class="xl65" style="height: 15pt; width: 114pt;" height="20" width="152"><br></td>
<td class="xl65" style="width: 44pt;" width="58"><br></td>
<td class="xl65" style="width: 44pt; background-color: rgb(255, 255, 51);" width="58"><br></td>
<td class="xl65" style="width: 44pt; background-color: rgb(255, 255, 51);" width="58"><br></td>
<td class="xl65" style="width: 91pt; background-color: rgb(255, 255, 51);" width="121">sqrt(C6i) (from ff)</td>
<td class="xl65" style="width: 85pt; background-color: rgb(255, 255, 51);" width="113">sqrt(C6j) (from ff)</td>
<td class="xl65" style="width: 89pt; background-color: rgb(255, 255, 51);" width="119">sqrt(C6i)*sqrt(C6j)</td>
<td class="xl65" style="width: 110pt;" width="146">value from tpr file</td>
</tr>
<tr style="height: 15pt;" height="20">
<td class="xl65" style="height: 15pt;" height="20">functype[154]=LJ14,</td>
<td class="xl65">c6A=</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">CH3</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">H</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">0.09805</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">0</td>
<td style="background-color: rgb(255, 255, 51);" class="xl66">0</td>
<td class="xl67">0.00E+00</td>
</tr>
<tr style="height: 15pt;" height="20">
<td class="xl65" style="height: 15pt;" height="20">functype[155]=LJ14,</td>
<td class="xl65">c6A=</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">CH3</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">CH1</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">0.09805</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">0.0779</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">0.007638095</td>
<td class="xl68">4.47E-03</td>
</tr>
<tr style="height: 15pt;" height="20">
<td class="xl65" style="height: 15pt;" height="20">functype[156]=LJ14,</td>
<td class="xl65">c6A=</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">C</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">CH2</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">0.04838</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">0.08642</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">0.004181</td>
<td class="xl68">3.33E-03</td>
</tr>
<tr style="height: 15pt;" height="20">
<td class="xl65" style="height: 15pt;" height="20">functype[157]=LJ14,</td>
<td class="xl65">c6A=</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">C</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">C</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">0.04838</td>
<td style="background-color: rgb(255, 255, 51);" class="xl65">0.04838</td>
<td style="background-color: rgb(255, 255, 51); color: rgb(255, 0, 0);" class="xl66">0.002340624</td>
<td style="color: rgb(255, 0, 0);" class="xl67">2.34E-03</td>
</tr>
</tbody></table><br>The values for N, C, O, H seems to be OK, but I have problems to get the same value, when CH1, CH2, CH3 are involved. Since I do not have too much experience, I would like to know how the value from the .tpr file can be derived.<br>
<br>The other entry for LJ potential is the short range term LJ_SR (.tpr file <br><br> ffparams:<br> atnr=11<br> ntypes=170<br> functype[0]=LJ_SR, c6= 9.61380266e-03, c12= 2.66462448e-05<br> functype[1]=LJ_SR, c6= 4.74365894e-03, c12= 1.14699596e-05<br>
functype[2]=LJ_SR, c6= 4.66325786e-03, c12= 5.16199998e-06<br><br>Unfortunately, I do not find the section where the function is assigned to a specific pair of interaction. Where are these functions assigned to a specific interaction? Furthermore, is it possible to distinguish between intra-nonbonded (solute-solute) and inter-bonded (water-solute) interaction?<br>
<br>For you this might be an easy question to answer, and you immediately realize there is a beginner at work, but nevertheless I would appreciate any help.<br><br>All the best<br>Otto <br>