Cutoff I set at 3.00 nm The distance between the two molecules is about 0.1 nm. The box is a cube of 20 nm
A bug perhaps? Marcelo. -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, May 04, 2006 3:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cgnr Marcelo A. Carignano wrote: > Thank you David, but there is no such a term in this case: > I see, make the cut-off larger. mdrun uses charge group based cutoff (see chap 4) and you are probably missing some interactions in the second case. > > $g_energy > .... > (deleted lines) > .... > > > Select the terms you want from the following list > ----------------------------------------------------- > LJ-(SR) Coulomb-(SR) Potential Kinetic-En. Total-Energy > Temperature Pressure-(bar) Vir-XX Vir-XY Vir-XZ > Vir-YX Vir-YY Vir-YZ Vir-ZX Vir-ZY > Vir-ZZ Pres-XX-(bar) Pres-XY-(bar) Pres-XZ-(bar) Pres-YX-(bar) > Pres-YY-(bar) Pres-YZ-(bar) Pres-ZX-(bar) Pres-ZY-(bar) Pres-ZZ-(bar) > #Surf*SurfTen Mu-X Mu-Y Mu-Z T-rest > > > Any other suggestion? > > Thank you, > Marcelo. > > > Marcelo A. Carignano wrote: >> Dear all: >> >> I'm running a test case defining all the interaction parameters in the >> topol.top file. My system consist of two NH3 molecules. >> Every thing goes well except for the role played by the "cgnr" values: >> Depending on how I assign these numbers the calculated Coulombic >> interaction changes. If I put the four atoms in the same group, the >> energy is not correct. If I put the four atoms in four different chnr's, >> the Coulombic interactions are OK: >> > > David wrote: > > > check the 14 energy. > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
