<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;">Dear Jochen,<br><br>Many thanx for your reply. It is really very nice to hear that it shouldn't make any big difference since I have already completed several lipid peptide simulations for ~20ns. :-)<br><br>thanks and regards,<br>Pri...<br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">----- Original Message ----<br>From: Jochen Hub <jhub@gwdg.de><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Sent: Thursday, 24 January, 2008 5:27:49 PM<br>Subject: Re: [gmx-users] comm_grps<br><br>In case of a lipid membrane simulation I would consider it as more <br>natural to keep the membrane in the center of the box, hence to apply <br>the com correction to
the lipids only. In the end it might, however,
not <br>make a big difference...<br><br>Jochen<br><br>priyanka srivastava wrote:<br>> Dear All,<br>><br>> I am a little confused with the application of<br>> comm_grps. I have a lipid-peptide system in which I am<br>> using the default values i.e. <br>><br>> comm_mode: linear<br>> nstcomm: 1<br>> comm_grps: whole system<br>><br>> Is there something wrong with defining comm_grps =<br>> whole system for the lipid-peptide case? Is it<br>> necessary to define lipid+peptide and solvent<br>> separately?<br>><br>> Eagerly waiting for the reply,<br>> Priyanka<br>><br>><br>><br>>
____________________________________________________________________________________<br>> Never miss a thing. Make Yahoo your home page. <br>> <a href="http://www.yahoo.com/r/hs" target="_blank">http://www.yahoo.com/r/hs</a><br>> _______________________________________________<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a 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 <br>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>><br>> .<br>><br>> <br><br><br>-- <br>************************************************<br>Jochen Hub<br>Max Planck Institute for Biophysical Chemistry<br>Computational biomolecular dynamics group<br>Am Fassberg 11<br>D-37077 Goettingen, Germany<br>Email: jhub[at]gwdg.de<br>************************************************ <br><br>_______________________________________________<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a
href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a 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 <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div><br></div></div><br>
<!--2--><hr size=1></hr> Did you know? You can CHAT without downloading messenger. <a href="http://in.rd.yahoo.com/tagline_webmessenger_2/*http://in.messenger.yahoo.com/webmessengerpromo.php"> Click here</a></body></html>