>From my own reading the Berger values are already scaled so to include them in gromacs by themselves no scaling would be required (like fudge=1.0). However OPLS 1-4 should be scaled by 0.5. So Chris Neale's method is to use fudge = 0.5 for OPLS and include the berger values twice. Here is a summary of what helped me understand the method from Chris Neale's posts:<br>
<br>"As the lipid.itp already has defined a pairtypes so that LJ 1-4 is scaled correctly (fudgeLJ is not applied to the values in [pairtypes] if there is a [ pairs ] section ) but the lipid fudgeQQ will be set to 0.5 instead of 1. If we divide the epsilon entries in the [ pairtypes ] of the lipid by two now both the LJ and coulombic 1-4 are exactly half of what they should be." <br>
<br>"Then include each entry in [pairs] twice so now LJ and coulombic 1-4 are both at what they should be."<br><br>This is a little confusing as you have to half the LJ value so you can double it later along with the Q.<br>
<br>Again:<br>"The pairs section defines both the Lj and the Q so we will have double of each. We only want double Q, since it is cut to half by the OPLS fudgeQQ value but not double epsilon(LJ) as it already has a special pairtypes section which is properly modified for 1-4 interactions."<br>
<br>More info:<br>defining [pairtypes]<br>automatically switches off the fudgeLJ option.<br><br>Hope this helps,<br>Oliver<br><br><br><div class="gmail_quote">2011/2/25 <span dir="ltr"><<a href="mailto:mircial@sjtu.edu.cn">mircial@sjtu.edu.cn</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Dear All:<br>
<br>
I am using GROMACS package to simulate membrane proteins. I plan to use Berger's united atom force field (Berger's UA FF) for lipids and OPLS_AA force field (OPLS_AA FF) for proteins.<br>
<br>
I have read the guide post kindly by Prof. Dr. Chris Neale in previous mailing lists very carefully. According to his guide, the following steps are needed:<br>
<br>
1). Added [atomtypes] from lipid.itp to ffoplsaanb.itp -- after changing c6/c12<br>
to sigma/epsilon. Also added atomtype H from olsa_369 to match H expected by<br>
pope.itp<br>
- sigma = (c12/c6)^1/6<br>
- epsilon = c6/(4*sigma^6)<br>
<br>
2). Added [pairtypes] from lipid.itp to ffoplsaanb.itp -- after changing c6/c12<br>
to sigma/epsilon. (gives effective fudgeLJ of 0.125). Also changed all reference<br>
to OW to opls_116 (opls spc water oxygen) and simply removed any with reference<br>
to HW as it will be zero regardless.<br>
<br>
3). Added [dihedraltypes] from lipid.itp to ffoplsaabon.itp.<br>
- Prior to running ensure that the non-RB dihedral does not exist for these<br>
groups.<br>
<br>
4). make a topology file like this:<br>
<br>
My questions are as follows:<br>
<br>
1, Berger's United atom force field scale LJ1-4 interaction by 0.125 and scale Coulombic1-4 interaction by 1.0. OPLS_AA FF scale both of them by 0.5, right? From the above changes, I find that the changes of the sigma or epsilon (or c6 and c12) is only associate with the LJ1-4 interaction. So, how the Coulombic1-4 interaction is scaled properly? Do I need additional changes?<br>
</blockquote><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
2, the non-bond interactions between the atoms from the lipid and the atoms from the protein are need to be calculated, right? My question is how these interactions are calculated? Does the changes in the [atomtypes]affect these interactions?<br>
<br>
3, How the non-bond interactions between the atoms from the lipid are calculated (e.g., the LJ and coulombic interactions)? Does the changes in the [atomtypes]affect these interactions?<br>
<br>
Thank you very much for your time and your kindness. I really appreciate your help.<br>
<br>
Regards<br>
<br>
Ruo-Xu Gu<br><font color="#888888">
<br>
<br>
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