Got it, Thank you, Mark! Best! Xueming On Wed, Jan 4, 2012 at 1:18 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> On 4/01/2012 4:43 PM, XUEMING TANG wrote: > >> Hello >> >> I am trying to adjust compound LJ parameter in oplsaa (sigma&epsilon) and >> also in Gromos (C6 and C12) forcefield for comparison. The original >> ffnonbonded.itp file in oplsaa.ff has no pair potential listed. While the >> original ffnonbonded.itp file in gromos**.ff listed all the pair >> potentials. If I change one atom potential, do I need to do anything to >> generate the new pair potential before running a simulation in opls-aa >> force field? Or how to generate the pair potentials? While for the case of >> gromos forcefield, the forcefield.itp file shows no pair potential will be >> generated. Is there any automatic ways to generate the modified LJ >> potentials? Should I list every possible LJ pair potentials in >> nonbonded.itp file? It looks like some very tedious work if several atoms >> are going to be modified. >> Also, what does fudge LJ and fudgeQQ mean in forcefield.itp file? Values >> of those two are different for OPLS and Gromos. >> > > In general, two force fields work differently and have their own > idiosyncrasies that will show up in how GROMACS implements them. When > modifying them, you should be sure to check the original literature and the > GROMACS manual and satisfy yourself how your changes will work. You should > search the manual for discussion of the use of gen-pairs and the fudge > values. I don't know why the list of [ nonbond_param ] values is exhaustive > - you'd think the combination rules could be used. In practice, you only > need to add parameters for interactions that can occur in your system, and > grompp will complain about those that it can't find. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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