<html><head><style type="text/css"><!-- DIV {margin:0px} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">Totally delete it from the itp shall be alright. Having a mass makes the atom visible to COM removal. What's the intention to make it invisible?<br><br>Yang Ye<br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">----- Original Message ----<br>From: Pradip Kumar Biswas <p.biswas@csuohio.edu><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Sent: Wednesday, June 21, 2006 10:18:29 PM<br>Subject: Re: [gmx-users] Re: How to ignore atoms during simulations??<br><br><div>I was wondering whether one can have atom types with zero charge, zero <br>vdw (C6=0, C12=0; Or sigma=0; epsilon=0), but with mass. Won't they be <br>invisible in the energy/force calculations (if they are not
connected <br>by any bonded interaction)?<br><br>pb.<br><br>On Jun 21, 2006, at 9:57 AM, Cesar Araujo wrote:<br><br>> Cesar Araujo wrote:<br>>> Hi,<br>>><br>>> Could anybody tell me how to modify an ITP file to ignore certain <br>>> atoms (as<br>> if<br>>> they were not there) during simulations? I've changed charge and <br>>> masses to<br>> 0.0<br>>> but I've got a lot of warnings during grompp preprocessing telling me <br>>> that<br>>> those atoms has zero mass and the program stops after certain numbers <br>>> of<br>>> warnings.<br>><br>>>> Well you've still got bonded and LJ interactions acting to create <br>>>> forces<br>>>> on particles with zero mass so it is no great surprise that things <br>>>> are<br>>>> breaking. Probably what you want to do is go back to square one and <br>>>> make<br>>>> topologies that don't have these
atoms, but you haven't described <br>>>> your<br>>>> chemistry, so we can't help you there.<br>><br>> Mark<br>><br>><br>> Well, my idea is to "delete" atoms and then "undelete" them without <br>> touching<br>> coordinates file. I guess that it could be done just touching topology <br>> files.<br>> Is it correct??? The results I'm looking for is to turn invisible some <br>> atoms.<br>><br>> Any suggestion???<br>><br>> Thanks in advance,<br>><br>> César.-<br>><br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> <a target="_blank" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><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 <a target="_blank"
href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>><br>><br>--<br>Pradip K. Biswas, PhD.<br>Research Associate, Department of Chemistry;<br>Cleveland State University, Ohio-44115<br>Phone: 1-216-875-9723<br><a target="_blank" href="http://comppsi.csuohio.edu/groups/people/biswas.html">http://comppsi.csuohio.edu/groups/people/biswas.html</a><br></div><div>I was wondering whether one can have atom types with zero charge, zero<br>vdw (C6=0, C12=0; Or sigma=0; epsilon=0), but with mass. Won't they be<br>invisible in the energy/force calculations (if they are not connected<br>by any bonded interaction)?<br><br><br>pb.<br><br><br>On Jun 21, 2006, at 9:57 AM, Cesar Araujo wrote:<br><br><br><excerpt>Cesar Araujo wrote:<br><br><excerpt>Hi,<br><br><br>Could anybody tell me how to modify an ITP file to ignore certain<br>atoms (as<br><br></excerpt>if<br><br><excerpt>they were not there) during
simulations? I've changed charge<br>and masses to<br><br></excerpt>0.0<br><br><excerpt>but I've got a lot of warnings during grompp preprocessing<br>telling me that<br><br>those atoms has zero mass and the program stops after certain numbers<br>of<br><br>warnings.<br><br></excerpt><br><br><excerpt><excerpt>Well you've still got bonded and LJ interactions<br>acting to create forces <br><br>on particles with zero mass so it is no great surprise that things are <br><br>breaking. Probably what you want to do is go back to square one and<br>make <br><br>topologies that don't have these atoms, but you haven't described your <br><br>chemistry, so we can't help you there.<br><br></excerpt></excerpt><br><br>Mark<br><br><br><br>Well, my idea is to "delete" atoms and then "undelete" them without<br>touching<br><br>coordinates file. I guess that it could be done just touching topology<br>files.<br><br>Is it correct??? The results I'm looking
for is to turn invisible some<br>atoms.<br><br><br>Any suggestion???<br><br><br>Thanks in advance,<br><br><br>César.-<br><br><br>_______________________________________________<br><br>gmx-users mailing list gmx-users@gromacs.org<br><br><a target="_blank" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br><br>Please don't post (un)subscribe requests to the list. Use the<br><br>www interface or send it to gmx-users-request@gromacs.org.<br><br>Can't post? Read <a target="_blank" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br><br><br><br></excerpt>--<br><br>Pradip K. Biswas, PhD.<br><br>Research Associate, Department of Chemistry;<br><br>Cleveland State University, Ohio-44115<br><br>Phone: 1-216-875-9723<italic><br><br><a target="_blank"
href="http://comppsi.csuohio.edu/groups/people/biswas.html">http://comppsi.csuohio.edu/groups/people/biswas.html</a> </italic><br><br></div><div>_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br><a target="_blank" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><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 <a target="_blank" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></div><br></div></div></body></html>