<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div><span class="e" id="q_12693ae257b51dc2_0">Hi !</span></div></blockquote>
<div> </div>
<div> </div>
<div>I am trying to reproduce results from reported polyacrylate simulations from literature. I have the values for bonded and non-bonded interaction parameters along with the the charges on atoms. I edited the charges and charge groups in the itp file. I would like to know whether in the [bonds } section, I can edit the itp file and give the force constants for the bonds instead of the non-bonded force constants (which the PRODRG provides). Similar edting for the angles and dihedrals sections would make the itp file suitable for running MD simulations. I ran MD simaultions with the existing itp file (with just editing the charges) , but simulation results were not comapring favorably with the reported values). </div>
<div> </div>
<div>I also would like to know, in the top file,</div>
<div>#include ffg43a1.itp</div>
<div>#include paa.itp</div>
<div> </div>
<div>the order should be as given above, or the reverse</div>
<div>#include paa.itp</div>
<div>#include ffg43a1.itp</div>
<div> </div>
<div>I read from the manual that, if any parameters are eneterd twice, the values which are read the second time will be taken.</div>
<div>In addition, I read FAQ for PRODRG, but was of no help in trying to understand the details of the ff parameters in the itp file it generates. From where I can get the information on the details of itp file generated by PRODRG.</div>
<div> </div>
<div>Thanking you for any help,</div>
<div> </div>
<div>Sulatha</div>
<div><br> </div>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div><span class="e" id="q_12693ae257b51dc2_0">Mark Abraham wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">On 03/02/10 15:55, sulatha M. S wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear gromas users,<br>I am new to gromacs and trying to run polyacrylate MD simulation. I<br>obtained an itp file using PRODRG (gromos 96 force-field parameters).<br>
When I compare with the same forcefield parameters in the gromacs/top<br>directory, they are far too off. For eg.<br><br>[ bonds ]<br>; ai aj fu c0, c1, ...<br>2 1 2 0.125 13400000.0 0.125 13400000.0 ; CAC OAD<br>2 3 2 0.125 13400000.0 0.125 13400000.0 ; CAC OAE<br>
4 2 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAC<br>4 5 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAA<br>4 6 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAG<br>7 6 2 0.153 7150000.0 0.153 7150000.0 ; CAH CAG<br>7 8 2 0.153 7150000.0 0.153 7150000.0 ; CAH CAI<br>
<br>As I understand, the function type should be 1 and c1 values should<br>correspond to the force constant for bond stretching. But here it<br>corresponds to the pair wise non bond parameters as listed in the<br>gromacs/top force-field file. Similarly,<br>
</blockquote><br>The bonded function type can have a whole range of values. See table in section 5.7.1 of the manual. That and the parameters, and the form of the target forcefield have to be considered as a whole in judging acceptability.<br>
<br>It's quite conceivable that the same numerical values are used in a bonded interaction (in [bonds] above) and forming the parameters in non-bonded interaction (in the [atomtypes] in the ffG96XXXbon.itp file) for in this case both pairs can represent quantities whose dimensions are length and energy respectively.<br>
<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">[ pairs ]<br>; ai aj fu c0, c1, ...<br>1 5 1 ; OAD CAA<br>1 6 1 ; OAD CAG<br>2 7 1 ; CAC CAH<br>3 5 1 ; OAE CAA<br>
3 6 1 ; OAE CAG<br>4 8 1 ; CAB CAI<br>4 11 1 ; CAB CAL<br>5 7 1 ; CAA CAH<br><br>there are no pair terms listed here in the pairs section.<br></blockquote><br>Some forcefields generate these solely from the [atomtype] data.<br>
<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">[ angles ]<br>; ai aj ak fu c0, c1, ...<br>1 2 3 2 126.0 770.0 126.0 770.0 ; OAD CAC OAE<br>1 2 4 2 117.0 635.0 117.0 635.0 ; OAD CAC CAB<br>
3 2 4 2 117.0 635.0 117.0 635.0 ; OAE CAC CAB<br>2 4 5 2 109.5 520.0 109.5 520.0 ; CAC CAB CAA<br>2 4 6 2 109.5 520.0 109.5 520.0 ; CAC CAB CAG<br>5 4 6 2 109.5 520.0 109.5 520.0 ; CAA CAB CAG<br>4 6 7 2 109.5 520.0 109.5 520.0 ; CAB CAG CAH<br>
For angles also the fu term is 2 instead of 1, although the angle and<br>the force constant parameters are correct.<br><br>Similar errors are there in the dihedrals section also.<br><br>This means I need to almost fully edit the itp file I got from PRODRG to<br>
proceed further. Thank you in advance for any help and please clarify<br>whether the itp file from PRODRG is unreliable even while using GROMOS96<br>force field ?<br></blockquote><br>There's no evidence of any error here. You should satisfy yourself from the contents of chapter 5 and the correct form of the GROMOS energy function that PRODRG is doing what you think it should. It looks to me like PRODRG is fine and you don't yet understand the form of what it should be producing. I suggest that you should do that learning.<br>
<br>Whether the numerical values will be sensible for MD simulations (as distinct from being expressed in a suitable form) is quite another question.<br></blockquote><br></span></div>And in addition, the most problematic section of a PRODRG topology is the [atoms] - the charges and charge groups are often unsatisfactory, requiring manual adjustment and validation (as you should, anyway, but the face-value parameters are often inconsistent with the original force field).<br>
<br>-Justin<br><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>
jalemkul[at]<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>========================================
<div><span class="e" id="q_12693ae257b51dc2_2"><br>-- <br>gmx-users mailing list <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></span></div></blockquote>
<br>