Dear all gmx users, developers, and Justin, I have tried the OPLS_136 and this is the force field that caused the 2 warnings during grompp and I had also try the other parameters. I think that should be needed a unique parameter development for this molecule. So, I am still "headache" about this.
Any guide n comments will be appreciated. Thank you --- On Sat, 7/5/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Subject: Re: segmentation fault during MD and develop parameter > To: [EMAIL PROTECTED] > Date: Saturday, July 5, 2008, 6:38 PM > It seems like there should be something special about that > location - a > tetrahedral center flanked by two rigid groups, but I > don't know just > how important that necessarily is. Have you tried just > assigning the > normal parameters for an alkane CH2 group (opls_136) to > your atom in > question? > > Just an idea, but I have no idea if this is a unique > situation that > requires unique parameter development. > > -Justin > > hhhh huan wrote: > > Dear all Gmx users n developers, > > I am happy and appreciate with all the help n > suggestions you all have given to me. > > > > Here is my molecule look likes.: > > > > C-C-C-C-C-C-C-C-C=C-C-C-C-C-C-C-C-C > > | > > O > > | > > C-C-C-C-C-C=C-(c)-C=C-C-C-C-C-C-C-C-C=O > > > > > > The problem that i faced now is the parameter of the > OPLS-AA force field for the carbon atom which is in the > bracket . I am now still looking for the solutions for this > problem. > > Any guide n comments will be appreciated. > > Thanks > > > > > > > > > > --- On Fri, 7/4/08, Justin A. Lemkul > <[EMAIL PROTECTED]> wrote: > > > > > >> From: Justin A. Lemkul <[EMAIL PROTECTED]> > >> Subject: [gmx-users] Re: segmentation fault during > MD and develop parameter > >> To: "Gromacs Users' List" > <[email protected]> > >> Date: Friday, July 4, 2008, 10:13 PM > >> hhhh huan wrote: > >> > >>> Dear all Gmx users n developers, > >>> > >>> I am a beginner of Gromacs user, hence I am > quite new > >>> > >> to the system..May i know how to develop the > missing > >> dihedral parameter? > >> > >>> Any guide n comments will be appreciated. > >>> Thanks > >>> > >>> > >>> > >> No one here is going to be able to help, aside > from the > >> standard, "Yes, > >> you can do it if you read the original paper for > the force > >> field you > >> want to use." If you describe your molecule > and what > >> the missing > >> parameter is (functional group, etc.), then maybe > someone > >> will have an > >> insight. > >> > >> Otherwise, you're in for some > parameterization, which > >> is not recommended > >> for the novice user. > >> > >> -Justin > >> > >> > >>> --- On Fri, 7/4/08, Justin A. Lemkul > >>> > >> <[EMAIL PROTECTED]> wrote: > >> > >>> > >>> > >>>> From: Justin A. Lemkul > <[EMAIL PROTECTED]> > >>>> Subject: Re: [gmx-users] segmentation > fault during > >>>> > >> MD > >> > >>>> To: [EMAIL PROTECTED], > "Discussion list > >>>> > >> for GROMACS users" > <[email protected]> > >> > >>>> Date: Friday, July 4, 2008, 6:41 PM > >>>> hhhh huan wrote: > >>>> > >>>> > >>>>> Dear gmx users and developers. > >>>>> > >>>>> I was running a simulation with 5 ns. > But it > >>>>> > >> stated > >> > >>>>> > >>>>> > >>>> "segmentation fault" at time > around 1 > >>>> > >> ns, and the > >> > >>>> simulation was stopped. > >>>> > >>>> > >>>>> By the way, i faced 2 warning during > running > >>>>> > >> the > >> > >>>>> > >>>>> > >>>> Grompp, it stated there:" warning 1 > No > >>>> > >> default > >> > >>>> Ryckaert-Bell types, using zeroes" > >>>> > >>>> > >>>>> File 'p1.top' , line > 209 > >>>>> warning 2 No default Ryckaert-Bell > types, > >>>>> > >> using > >> > >>>>> > >>>>> > >>>> zeroes" > >>>> > >>>> > >>>>> File 'p1.top' , line > 210 > >>>>> > >>>>> > >>>>> i know that thses are the missing > force field > >>>>> > >>>>> > >>>> parameter at the indicated line,but i keep > on > >>>> > >> running the > >> > >>>> simulation and the segmentation fault > appeared > >>>> > >> because i > >> > >>>> cant find any force field that is suitable > for the > >>>> particular atoms. However, I manage to > finish the > >>>> > >> energy > >> > >>>> minimization. > >>>> > >>>> > >>>>> So, is it the segmentation fault has > anything > >>>>> > >> to do > >> > >>>>> > >>>>> > >>>> with the 2 warning? or there is any other > way to > >>>> > >> solve my > >> > >>>> problems? > >>>> > >>>> > >>>>> > >>>>> > >>>>> > >>>> You need to find/develop parameters for > the > >>>> > >> missing > >> > >>>> dihedral > >>>> parameters. Running a simulation with > missing > >>>> > >> information > >> > >>>> will likely > >>>> lead to inaccurate/questionable results. > >>>> > >>>> As for whether that directly lead to the > >>>> > >> segmentation > >> > >>>> fault, that's > >>>> difficult to diagnose, but I would start > by > >>>> > >> getting the > >> > >>>> missing > >>>> parameters to eliminate it as a > possibility. > >>>> > >>>> -Justin > >>>> > >>>> > >>>> > >>>>> Thanks a lot > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >> _______________________________________________ > >> > >>>>> gmx-users mailing list > >>>>> > >> [email protected] > >> > >> 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 > >>>> > >>>> > >>>>> > >>>>> > >>>>> > >>>> -- > >>>> ======================================== > >>>> > >>>> 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 > >> > >>>> ======================================== > >>>> > >>>> > >>> > >>> > >>> > >>> > >> -- > >> ======================================== > >> > >> 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 [email protected] > >> 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 > >> > > > > > > > > > > > > -- > ======================================== > > 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 [email protected] 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
