PS: My previous email was accidentally sent from the gmail account of my colleague, who uses the same workstation. My apologies. This is just a disclaimer on her behalf.
On Mon, May 5, 2008 at 11:34 AM, himanshu khandelia <[EMAIL PROTECTED]> wrote: > Hi, > > I am trying to run a simulation of a POPC bilayer mixed with some > mono-anionic Phosphatidic acid (POPA) , where the choline group is > replaced by a hydrogen atom. However, the energy of my simulation box > diverges, and I am trying to fix the problem. I also tried running a > simulation of PA solvated in water and a single sodium ion, but even > that does not work. I will try to provide as much detail as possible, > I hope someone can help point out some obvious error which I have not > been able to debug over 3 days. In the simulation of a single PA > molecule in water, MDRUN keeps complaining that the distance between > atoms H1 and O4 is very high (> 4 nm or so). The problem probably lies > in my topology, possibly in the bonded interactions? > > Thank you very very much for all suggestions. > > The headgroup of phosphatidic acid in my topology looks something like this: > > H1 > | > (-) O4 O2 > \ / > P3 (+) > / \ > (-)O5 O6 > | > C7-----etc..... (rest of lipid) > > The same region in the POPC topology looks something like this: > > C6-----etc (choline group) > | > (-) O9 O7 > \ / > P8 (+) > / \ > (-)O10 O11 > | > C12---------etc .... (rest of lipid) > > > Thus, only one new atom type, a H-atom was introduced. I replaced the > C6 of POPC by H1 on POPA. O7, P8, O9 were replaced by O2, P3, O4 and > so on (so atom indices differ by a factor of 5) > > In the following, I have copy-pasted the topology of POPA and POPC for > the above regions. The topology for POPC is the one on Tieleman's > webpage, of course. My topology is directly derived from it. > > > ############################################################################################### > ###### FOR POPA ####### > [ atoms ] > ; nr type resnr residu atom cgnr charge mass > 1 LHO 1 PAPA H1 1 0.400 > 1.0080 ; this is the new atom type, I defined it in the lipid.itp file > and also described non-bonded interactions and pairtypes for this > atom. > 2 LOS 1 PAPA O2 1 -0.600 15.9994 ; > 3 LP 1 PAPA P3 1 1.500 30.9738 > 4 LOM 1 PAPA O4 1 -0.800 15.9994 > 5 LOM 1 PAPA O5 1 -0.800 15.9994 > 6 LOS 1 PAPA O6 1 -0.700 > 15.9994 ; qtot:-1 > 7 LC2 1 PAPA C7 2 0.400 14.0270 > > [bonds ] > ; ai aj funct > 1 2 1 0.10000E+00 0.31380E+06 > 2 3 1 0.16100E+00 0.25100E+06 > 3 4 1 0.14800E+00 0.37660E+06 > 3 5 1 0.14800E+00 0.37660E+06 > 3 6 1 0.16100E+00 0.25100E+06 > 6 7 1 0.14300E+00 0.25100E+06 > ....etc > [ pairs ] > ; ai aj funct > 1 4 1 > 1 5 1 > 1 6 1 > 2 7 1 > 3 8 1 > 4 7 1 > .... etc .... > > [ angles ] > ; ai aj ak funct > 1 2 3 1 0.10960E+03 0.39750E+03 > 2 3 4 1 0.10960E+03 0.39750E+03 > 2 3 5 1 0.10960E+03 0.39750E+03 > 2 3 6 1 0.10300E+03 0.39750E+03 > 3 6 7 1 0.12000E+03 0.39750E+03 > 4 3 5 1 0.12000E+03 0.58580E+03 > 4 3 6 1 0.10960E+03 0.39750E+03 > 5 3 6 1 0.10960E+03 0.39750E+03 > > [ dihedrals ] > ; ai aj ak al funct phi0 cp mult > 1 2 3 6 1 0.0 1.05 3 > 1 2 3 6 1 0.0 3.14 2 > 2 3 6 7 1 0.0 1.05 3 > 2 3 6 7 1 0.0 3.14 2 > > ##################################################################################### > > > ##################################################################################### > ###### FOR POPC ####### > > [ atoms ] > ; nr type resnr residu atom cgnr charge mass > > ; 1 to 5 are from the choline group > > 6 LC2 1 POPC C6 1 0.4000 > 14.0270 ; qtot:1.0 > 7 LOS 1 POPC O7 1 -0.800 > 15.9994 ; qtot:0.54 > 8 LP 1 POPC P8 1 1.700 > 30.9738 ; qtot:2.3 > 9 LOM 1 POPC O9 1 -0.800 > 15.9994 ; qtot:1.5 > 10 LOM 1 POPC O10 1 -0.800 > 15.9994 ; qtot:0.7 > 11 LOS 1 POPC O11 1 -0.700 15.9994 ; > qtot:0 > 12 LC2 1 POPC C12 2 0.400 > 14.0270 ; qtot:0.08 > > [ bonds ] > ; ai aj funct > 6 7 1 0.14300E+00 0.25100E+06 > 7 8 1 0.16100E+00 0.25100E+06 > 8 9 1 0.14800E+00 0.37660E+06 > 8 10 1 0.14800E+00 0.37660E+06 > 8 11 1 0.16100E+00 0.25100E+06 > 11 12 1 0.14300E+00 0.25100E+06 > > [ pairs ] > ; ai aj funct > 4 7 1 > 5 8 1 > 6 9 1 > 6 10 1 > 6 11 1 > 7 12 1 > > [ angles ] > ; ai aj ak funct > 6 7 8 1 0.12000E+03 0.39750E+03 > 7 8 9 1 0.10960E+03 0.39750E+03 > 7 8 10 1 0.10960E+03 0.39750E+03 > 7 8 11 1 0.10300E+03 0.39750E+03 > 8 11 12 1 0.12000E+03 0.39750E+03 > 9 8 10 1 0.12000E+03 0.58580E+03 > 9 8 11 1 0.10960E+03 0.39750E+03 > 10 8 11 1 0.10960E+03 0.39750E+03 > > > [ dihedrals ] > ; ai aj ak al funct phi0 cp mult > 6 7 8 11 1 0.0 1.05 3 > 6 7 8 11 1 0.0 3.14 2 > 7 8 11 12 1 0.0 1.05 3 > 7 8 11 12 1 0.0 3.14 2 > > ############################################################################################### > _______________________________________________ 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
