Hi All I have gromacs files generated using acpype tool acting on Amber files originally. I need to know the meaning of certain terms in that *.top file (email with attachment of .top file got blocked due to attachment). Unfortunately, I can't find on the web, any material regarding that. It would be great, if anyone could comment on the following.
*1. What is the meaning of terms under defaults option at the top of the file (pasted below)?* [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 * 2a. ** Is atomtypes section needed? (sample .top file on gromacs website does not have it) (pasted after 2b question)**In this atomtypes section, the Amber2gromacs tool keeps mass and charge of each atom as zero. Would a simulation with these places zero be a valid simulation **?* My guess is yes. THis is since, corresponding values are available later in atoms section. The purpose of asking this question is that I have to be sure of the runs I have made, that nothing has gone wrong in having those zeros. * 2b.I see several enigmatic terms such as bond type p type, Amb. Can you explain these terms, if they are necessary at all? Why last two columns for Amb?* (part of the data for both 2a and 2b pasted below) [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb Ti Ti 0.00000 0.00000 A 1.39461e-01 6.08772e-02 ; 0.78 0.0145 OT OT 0.00000 0.00000 A 2.87832e-01 8.29687e-02 ; 1.62 0.0198 HW HW 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 *4.WHat is cgnr? how is it different from nr? (it appears in atoms section, example below)* nr type resi res atom cgnr charge mass ; qtot bond_type 1 Ti 1 iO2 TI 1 1.691002 47.86700 ; qtot 1.691 Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.