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