Hi Justin thanks for your email, yes I used the -pp option to print out the file I showed here. I am using gromacs-3.3.3 and I compiled it just doing the typical ./configure make make install and I checked and it's using cc as a compiler.
What I was trying to do is to run a calculation using Gromos forcefield in another program I have and I was trying to debug it by trying to match the energy coming from gromacs using that same forcefield. I tried the -pp option in grompp to show explicitly the parameters being used during the calculation and that is how I got the file I showed. I tried the gmxdump and that seems to be ok. I wrote my conversion file based on that file so now it works fine :). Just one last question, in the PRODRG website the gromacs topology files generated have function 1 for both angles and bonds, that means that the functions to be used are the regular harmonic form for both, right? Thanks a lot for your time!!! Romelia > > > Romelia Salomon wrote: >> Hi >> >> I am trying to set a calculation based on the GROMOS force field in a >> program I have and I am using GROMACS to generate the (starting) input >> files for me. From reading the manual I know that GROMOS uses a fourth >> power potential (type 2) for bonds and a cosine based angle potential >> (type 2), but I noticed that when using grompp to include the values for >> the parameters explicitly it changes the type from 2 to 1, for example: >> >> topology file before grompp >> [ bonds ] >> ; ai aj funct c0 c1 c2 >> c3 >> 1 2 2 gb_2 >> 1 3 2 gb_2 >> 1 4 2 gb_2 >> 1 5 2 gb_20 >> 5 6 2 gb_26 >> 5 10 2 gb_26 >> after using grompp > > This would be from the -pp flag of grompp? > >> [ bonds ] >> ; ai aj tp parameters >> N H1 1 0.1 1.87e+07 >> N H2 1 0.1 1.87e+07 >> N H3 1 0.1 1.87e+07 >> N CA 1 0.147 8.71e+06 >> CA CB 1 0.153 7.15e+06 >> CA C 1 0.153 7.15e+06 >> > > Which version of Gromacs are you using? I'm using 3.3.3, and mine works > just > fine (bond type is 2). Furthermore, it's odd that grompp is including > atom > names instead of numbers...unless you've interpreted what the output > really is > and transcribed it differently :) > > If grompp is changing these, then perhaps it's a bug. Note that weird > behavior > arises when Gromacs is compiled with gcc 4.1.x, as has been beaten to > death on > this list :) Without knowing more about your system, this is pure > speculation > and may not be worth anything. > >> Is this right? Also, for clarification, I know Gromacs uses kj/mol and >> nm >> as units, so does that mean that the values included in the ff*.itp >> files >> under the share/top/ directory are in those units? >> > > The units are all consistent. > > -Justin > >> Also I noticed that the .itp files for bonding interactions in >> gmxbon.itp >> have declared a type 1 function which would be the regular harmonic one. >> >> Sorry for the very basic questions, but I wanted to be certain about >> this >> things, thanks!! >> >> Romelia >> >> Thanks! >> >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > -- **************************************** Romelia Salomon Miller Group 316 Noyes Chemistry Department Caltech _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
