I went through the LINCS manual . But, I am still struggling with coming up with the idea of putting correct constraint to maintain the rigidity of tetrahedral molecule . I seem to understand from your suggestion that the tetrahedral can be seen as a combination of 4 coupled triangles.( or am I still wrong about it ?) In that case, am I supposed to use multiple settle to keep the molecule in a tetrahedral fashion ? I am sorry but if you can explain it in bit more details, I might get the point.
________________________________ From: Mark Abraham <mark.abra...@anu.edu.au> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Wed, April 27, 2011 11:14:34 PM Subject: Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 1:54 PM, Sanku M wrote: Hi, > I tried to keep the geometry of the BF4 fixed by using constraints >using lincs. But , unfortunately, my simulation is crashing >immediately and if I try minimization with only 2 molecules, it >provides a lot of LINCS warning and generate a lot of step*.pdb file >. >If I try to visualize the minimized snapshot in VMD, it looks like >all >the distances I tried to constrain decreased drastically. Finally, >trying MD run with this "minimized" configuration results in >crashing >due to bad contacts. > > > I am sure I am doing something wrong and it might be that my itp > file >is wrong . So any help will be highly appreciated. >Here is the details of what I did. > > > The geometry of the molecule is tetrahedral with B at the > center >and 4 F atoms is surrounding it in a tetrahedral manner. >I first generated a itp file for BF4 which is shown below: I first >got >the LJ parameters and charges for B and F atom and put them in >ffoplsnb.itp file as new atom types opls_1014 and opls_1015 >. Initially I tried to put contsraint along all bonds ( i.e among F >atoms as well ). But, grompp provides warning that number of >constraint is more than number of degrees of freedom. So, I reduced >number of constraints by only putting constraint among B and F. But, >it did not work either. > > Sure, you need as many constraints as http://en.wikipedia.org/wiki/Degrees_of_freedom_%28physics_and_chemistry%29 You should also do your homework about using LINCS and coupled triangles of constraints, as I suggested last time. Mark Here is the .itp file I wrote for rigid BF4 . It will be great if someone can point me what I am doing wrong. > > > [ moleculetype ] >; molname nrexcl >BF4 3 > > >[ atoms ] >#ifdef _FF_OPLS > 1 opls_1014 1 BF4 B 1 0.8276 > 2 opls_1015 1 BF4 F1 1 -0.4569 > 3 opls_1015 1 BF4 F2 1 -0.4569 > 4 opls_1015 1 BF4 F3 1 -0.4569 > 5 opls_1015 1 BF4 F4 1 -0.4569 >#endif >[ constraints ] > 1 2 1 0.146 > 1 3 1 0.146 > 1 4 1 0.146 > 1 5 1 0.146 > ; 2 3 1 0.238 >; 2 4 1 0.238 >; 2 5 1 0.238 >; 3 4 1 0.238 >; 3 5 1 0.238 >; 4 5 1 0.238 > > >[ exclusions ] >1 2 3 4 5 >2 1 3 4 5 >3 1 2 4 5 >4 1 2 3 5 >5 1 2 3 4 > > > > > ________________________________ From: Mark Abraham <mark.abra...@anu.edu.au> >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Sent: Wed, April 27, 2011 8:39:23 PM >Subject: Re: [gmx-users] rigid tetrahedral molecule > >On 4/28/2011 11:25 AM, Justin A. Lemkul wrote: >> >> >> Sanku M wrote: >>> Hi, >>> I am interested in simulating a anionic molecule BF4(-) ( >>> Boron >>>tetrafluoride). In the paper which developed the parameters for >>>this molecule, it is mentioned that it has been used as 'rigid' >>>molecule i.e the molecule only has non-bonding interaction but >>>there >>>was no intramolecular motion as the geometry was fixed. >>> I am trying to simulate this molecule in gromacs treating it >>> as >>>rigid. But, I was looking for best way to 'rigidify' this >>>molecule. >>> >>> I was wondering whether using LINCS to constrain all B-F and >>> F-F >>>bonds will be good enough . Or, Should I use virtual sites ? If >>>I >>>really need to use virtual site, will it be something like TIP5P >>>water model ? >>> Can someone suggest the best wayout ? >>> >> >> Constraints should do the trick, but probably the best approach >> is >>to simply contact the authors who developed the model and ask how >>they did it. Then you know you're exactly reproducing what they >>did. > >Yep. > >Be aware that the coupled constraints make life tricky, and you >should read up in the manual and literature for how best to use >P-LINCS in such cases. Algorithms like SETTLE for rigid water >exist >for a reason... > >Mark > > > >-- gmx-users mailing list gmx-users@gromacs.org >http://lists.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at >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 >
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