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Hi,<br><br>There are two separate issues here.<br><br>One is the charge groups assignment with AMBER.<br>I think that in Gromacs we, in general, do not want all atoms in separate charge groups,<br>but we want to include at least the hydrogens in a charge group with the heavy atom.<br>We would also like the option to make every atom a single charge group,<br>but pdb2gmx of 4.1 already has an option for this.<br>Since the AMBER force fields are currently not in the Gromacs package,<br>we don't have control over the charge group assignment.<br><br>The second issue is the crashing of the simulations.<br>I don't see why simulations would crash with the slightly strange charge group assignment.<br>But it sounds like there is a bug somewhere.<br>I suspect it could happen when an NH3 group is partially over a box edge.<br>This is strange though, since I think I check all nasty combinations of vsite generation<br>and charge groups.<br><br>I already got such a file from Bert.<br><br>Berk<br><br>> Date: Wed, 30 Sep 2009 15:35:42 +0200<br>> From: jochen@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes<br>> <br>> Hi,<br>> <br>> I have been trying to use vsites with AMBER99SB, but the simulation <br>> frequently cashes after a few hundred ps with the suspects (lincs <br>> warnings, 1-4 distance error). I could pinpoint the problem to erroneous <br>> charge group assignments generated by pdb2gmx at the NH3 group at the <br>> N-terminus. The following charge group assignments caused the error:<br>> <br>> ; nr type resnr residue atom cgnr charge mass <br>> 1 MNH3 1 NASN MN1 1 0 8.517 ; <br>> qtot 0<br>> 2 MNH3 1 NASN MN2 1 0 8.517 ; <br>> qtot 0<br>> 3 amber99_39 1 NASN N 1 0.1801 0 ; <br>> qtot 0.1801<br>> 4 amber99_17 1 NASN H1 2 0.1921 0 ; <br>> qtot 0.3722<br>> 5 amber99_17 1 NASN H2 2 0.1921 0 ; <br>> qtot 0.5643<br>> 6 amber99_17 1 NASN H3 2 0.1921 0 ; <br>> qtot 0.7564<br>> 7 amber99_11 1 NASN CA 3 0.0368 13.018 ; <br>> qtot 0.7932<br>> ...<br>> <br>> The NH3 groups in the lysines were fine and did not cause any error. The <br>> only difference compared to the N-terminus is that each of the three H <br>> in the NH3 has its own charge group, but the vsites and the N are still <br>> in the same CG:<br>> <br>> 30 amber99_11 2 LYP CE 29 -0.0143 14.026 ; <br>> qtot 0.9937<br>> 31 amber99_28 2 LYP HE1 30 0.1135 0 ; <br>> qtot 1.107<br>> 32 amber99_28 2 LYP HE2 31 0.1135 0 ; <br>> qtot 1.221<br>> 33 MNH3 2 LYP MNZ1 32 0 8.517 ; <br>> qtot 1.221<br>> 34 MNH3 2 LYP MNZ2 32 0 8.517 ; <br>> qtot 1.221<br>> 35 amber99_39 2 LYP NZ 32 -0.3854 0 ; <br>> qtot 0.8353<br>> 36 amber99_17 2 LYP HZ1 33 0.34 0 ; <br>> qtot 1.175<br>> 37 amber99_17 2 LYP HZ2 34 0.34 0 ; <br>> qtot 1.515<br>> 38 amber99_17 2 LYP HZ3 35 0.34 0 ; <br>> qtot 1.855<br>> <br>> Alternatively, I have also tried to give every single atom (including <br>> the vsites MN??) a separate charge group, which also worked fine.<br>> <br>> 1)<br>> So, is there any reason why the dummies should be in the same CG as the <br>> nitrogen? Or should it be fine just to assign a separate CG to every atom?<br>> <br>> 2)<br>> Is a bug report appreciated on that issue?<br>> <br>> Best,<br>> <br>> Jochen<br>> <br>> <br>> -- <br>> ---------------------------------------------------<br>> Dr. Jochen Hub<br>> Molecular Biophysics group<br>> Dept. of Cell & Molecular Biology<br>> Uppsala University. Box 596, 75124 Uppsala, Sweden.<br>> Phone: +46-18-4714451 Fax: +46-18-511755<br>> ---------------------------------------------------<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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