<div id=":6z" class="ii gt"><div>Dear gromas users,</div>
<div> </div>
<div>I am new to gromacs and trying to run polyacrylate MD simulation.
I obtained an itp file using PRODRG (gromos 96 force-field parameters).
When I compare with the same forcefield parameters in the gromacs/top
directory, they are far too off. For eg. </div>
<div> </div>
<div>
<p style="margin: 0in 0in 0pt;"><font size="2"><font face="Courier New">[ bonds ]<br>; ai<span> </span>aj<span> </span>fu<span> </span>c0, c1, ...<br>
<span> </span>2<span> </span>1<span> </span>2<span> </span>0.125<span> </span>13400000.0<span> </span>0.125<span> </span>13400000.0 ;<span> </span>CAC<span> </span>OAD<span> </span><br>
<span> </span>2<span> </span>3<span> </span>2<span> </span>0.125<span> </span>13400000.0<span> </span>0.125<span> </span>13400000.0 ;<span> </span>CAC<span> </span>OAE<span> </span><br>
<span> </span>4<span> </span>2<span> </span>2<span> </span>0.153<span> </span>7150000.0<span> </span>0.153<span> </span>7150000.0 ;<span> </span>CAB<span> </span>CAC<span> </span><br>
<span> </span>4<span> </span>5<span> </span>2<span> </span>0.153<span> </span>7150000.0<span> </span>0.153<span> </span>7150000.0 ;<span> </span>CAB<span> </span>CAA<span> </span><br>
<span> </span>4<span> </span>6<span> </span>2<span> </span>0.153<span> </span>7150000.0<span> </span>0.153<span> </span>7150000.0 ;<span> </span>CAB<span> </span>CAG<span> </span><br>
<span> </span>7<span> </span>6<span> </span>2<span> </span>0.153<span> </span>7150000.0<span> </span>0.153<span> </span>7150000.0 ;<span> </span>CAH<span> </span>CAG<span> </span><br>
<span> </span>7<span> </span>8<span> </span>2<span> </span>0.153<span> </span>7150000.0<span> </span>0.153<span> </span>7150000.0 ;<span> </span>CAH<span> </span>CAI<span> </span><br>
<span> </span></font></font></p>
<p style="margin: 0in 0in 0pt;"><font size="2"><font face="Courier New"><span></span></font></font> </p>
<p style="margin: 0in 0in 0pt;"><font size="2"><font face="Courier New"><span>As
I understand, the function type should be 1 and c1 values should
correspond to the force constant for bond stretching. But here it
corresponds to the pair wise non bond parameters as listed in the
gromacs/top force-field file. Similarly,</span></font></font></p>
<p style="margin: 0in 0in 0pt;"><font size="2"><font face="Courier New"><span></span></font></font> </p><font size="2"><font face="Courier New"><span>
<p style="margin: 0in 0in 0pt;"><font size="2"><font face="Courier New">[ pairs ]<br>; ai<span> </span>aj<span> </span>fu<span> </span>c0, c1, ...<br>
<span> </span>1<span> </span>5<span> </span>1<span> </span>;<span> </span>OAD<span> </span>CAA<span> </span><br>
<span> </span>1<span> </span>6<span> </span>1<span> </span>;<span> </span>OAD<span> </span>CAG<span> </span><br>
<span> </span>2<span> </span>7<span> </span>1<span> </span>;<span> </span>CAC<span> </span>CAH<span> </span><br>
<span> </span>3<span> </span>5<span> </span>1<span> </span>;<span> </span>OAE<span> </span>CAA<span> </span><br>
<span> </span>3<span> </span>6<span> </span>1<span> </span><span> </span>;<span> </span>OAE<span> </span>CAG<span> </span><br>
<span> </span>4<span> </span>8<span> </span>1<span> </span>;<span> </span>CAB<span> </span>CAI<span> </span><br>
<span> </span>4<span> </span>11<span> </span>1<span> </span>;<span> </span>CAB<span> </span>CAL<span> </span><br>
<span> </span>5<span> </span>7<span> </span>1<span> </span>;<span> </span>CAA<span> </span>CAH<span> </span></font></font></p>
<font size="2"><font face="Courier New"><span></span></font></font></span></font></font></div>
<div><font size="2"><font face="Courier New"><span><font size="2"><font face="Courier New"><span>there are no pair terms listed here in the pairs section.</span></font></font></span></font></font></div>
<div><font size="2"><font face="Courier New"><span><font size="2"><font face="Courier New"><span></span></font></font></span></font></font> </div>
<div><font size="2"><font face="Courier New"><span><font size="2"><font face="Courier New"><span></span></font></font></span></font></font><font size="2"><font face="Courier New"><span>
<p style="margin: 0in 0in 0pt;"><font size="2"><font face="Courier New">[ angles ]<br>; ai<span> </span>aj<span> </span>ak<span> </span>fu<span> </span>c0, c1, ...<br>
<span> </span>1<span> </span>2<span> </span>3<span> </span>2<span> </span>126.0<span> </span>770.0<span> </span>126.0<span> </span>770.0 ;<span> </span>OAD<span> </span>CAC<span> </span>OAE<span> </span><br>
<span> </span>1<span> </span>2<span> </span>4<span> </span>2<span> </span>117.0<span> </span>635.0<span> </span>117.0<span> </span>635.0 ;<span> </span>OAD<span> </span>CAC<span> </span>CAB<span> </span><br>
<span> </span>3<span> </span>2<span> </span>4<span> </span>2<span> </span>117.0<span> </span>635.0<span> </span>117.0<span> </span>635.0 ;<span> </span>OAE<span> </span>CAC<span> </span>CAB<span> </span><br>
<span> </span>2<span> </span>4<span> </span>5<span> </span>2<span> </span><span> </span>109.5<span> </span>520.0<span> </span>109.5<span> </span>520.0 ;<span> </span>CAC<span> </span>CAB<span> </span>CAA<span> </span><br>
<span> </span>2<span> </span>4<span> </span>6<span> </span>2<span> </span>109.5<span> </span>520.0<span> </span>109.5<span> </span>520.0 ;<span> </span>CAC<span> </span>CAB<span> </span>CAG<span> </span><br>
<span> </span>5<span> </span>4<span> </span>6<span> </span>2<span> </span>109.5<span> </span>520.0<span> </span>109.5<span> </span>520.0 ;<span> </span>CAA<span> </span>CAB<span> </span>CAG<span> </span><br>
<span> </span>4<span> </span>6<span> </span>7<span> </span>2<span> </span>109.5<span> </span>520.0<span> </span>109.5<span> </span>520.0 ;<span> </span>CAB<span> </span>CAG<span> </span>CAH<span> </span></font></font><br>
For angles also the fu term is 2 instead of 1, although the angle and the force constant parameters are correct.</p>
<p style="margin: 0in 0in 0pt;">Similar errors are there in the dihedrals section also.</p>
<p style="margin: 0in 0in 0pt;"> </p>
<p style="margin: 0in 0in 0pt;">This means I need to almost fully edit
the itp file I got from PRODRG to proceed further. Thank you in advance
for any help and please clarify whether the itp file from PRODRG is
unreliable even while using GROMOS96 force field ? </p>
<p style="margin: 0in 0in 0pt;"> </p>
<p style="margin: 0in 0in 0pt;">Thanking you,</p>
<p style="margin: 0in 0in 0pt;"> </p>
<p style="margin: 0in 0in 0pt;">Dr. M. S Sulatha</p>
<p style="margin: 0in 0in 0pt;">Women Scientist</p>
<p style="margin: 0in 0in 0pt;">Chemical Engineering Dept.</p>
<p style="margin: 0in 0in 0pt;">IIT-Madras, Chennai</p>
<p style="margin: 0in 0in 0pt;">India</p>
<p style="margin: 0in 0in 0pt;"> </p>
<p style="margin: 0in 0in 0pt;"> </p></span></font></font></div>
<p style="margin: 0in 0in 0pt;"><br></p>
</div>