GROMACS version:2021
GROMACS modification: Yes/No
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I did the energy minimization for the my membrane and nanoparticle complex, but after this step my structure disintegrated. I removed the pbc condition using the following command but the problem still exists. please guide me.
gmx trjconv -f em.gro -s em.tpr -o nopbc.pdb -ur compact -center -pbc nojump
Hi,
I do not aspect large conformational changes occuring during energy minimization of a system in condensed phase. I suggest to check the quality of the starting structure.
Best regards
Alessandra
its my membrane along with nanoparticle.
I found that after ionization, the structure of the membrane forms a structural change and the phosphor groups have a displacement.
Did grompp issue any warnings about mismatched atom names between the coordinates and topology that you overrode with -maxwarn? It appears to me the atom identities have been shuffled, which will happen if your topology is constructed incorrectly with respect to the coordinate file.
yes i get one warning and upload below.ionization warning.mdp (6.9 KB)
The atoms in the coordinate file and topology (as listed in [molecules]) have to be in the same order. Fix that, otherwise your system is impossibly broken.
thanks for your response. everything is ok and order of queries is same in coordinate and topology file.
grompp is complaining about atom order in the lipids. Something has changed there.
I generated membrane by charmm-gui then add nanoparticle to this and parametrized complex by gromacs but can’t understand cause of this problem, i need to your recommendation.
Without full access to all of your files, there’s nothing more I can tell you than what I already have. Something you have done to the coordinates has changed their order relative to what the topology specifies. The problem is explicitly in the lipids:
atom name 2 in topol.top and input.gro does not match (C13 - P) atom name 2 in topol.top and input.gro does not match (C13 - P) atom name 3 in topol.top and input.gro does not match (H13A - C1) atom name 3 in topol.top and input.gro does not match (H13A - C1) atom name 4 in topol.top and input.gro does not match (H13B - C2) atom name 4 in topol.top and input.gro does not match (H13B - C2) atom name 5 in topol.top and input.gro does not match (H13C - C3) atom name 5 in topol.top and input.gro does not match (H13C - C3) atom name 6 in topol.top and input.gro does not match (C14 - C11) atom name 6 in topol.top and input.gro does not match (C14 - C11) atom name 7 in topol.top and input.gro does not match (H14A - O11) atom name 7 in topol.top and input.gro does not match (H14A - O11) atom name 8 in topol.top and input.gro does not match (H14B - C12) atom name 8 in topol.top and input.gro does not match (H14B - C12) atom name 9 in topol.top and input.gro does not match (H14C - O12) atom name 9 in topol.top and input.gro does not match (H14C - O12) atom name 10 in topol.top and input.gro does not match (C15 - C13) atom name 10 in topol.top and input.gro does not match (C15 - C13) atom name 11 in topol.top and input.gro does not match (H15A - O13) atom name 11 in topol.top and input.gro does not match (H15A - O13) atom name 12 in topol.top and input.gro does not match (H15B - C14) atom name 12 in topol.top and input.gro does not match (H15B - C14) atom name 13 in topol.top and input.gro does not match (H15C - O14) atom name 13 in topol.top and input.gro does not match (H15C - O14) atom name 14 in topol.top and input.gro does not match (C12 - C15) atom name 14 in topol.top and input.gro does not match (C12 - C15) atom name 15 in topol.top and input.gro does not match (H12A - C21) atom name 15 in topol.top and input.gro does not match (H12A - C21) atom name 16 in topol.top and input.gro does not match (H12B - O21) atom name 16 in topol.top and input.gro does not match (H12B - O21) atom name 17 in topol.top and input.gro does not match (C11 - C22) atom name 17 in topol.top and input.gro does not match (C11 - C22) atom name 18 in topol.top and input.gro does not match (H11A - O22) atom name 18 in topol.top and input.gro does not match (H11A - O22) atom name 19 in topol.top and input.gro does not match (H11B - C23) atom name 19 in topol.top and input.gro does not match (H11B - C23) atom name 20 in topol.top and input.gro does not match (P - C24) atom name 20 in topol.top and input.gro does not match (P - C24) atom name 21 in topol.top and input.gro does not match (O13 - C25) atom name 21 in topol.top and input.gro does not match (O13 - C25) (more than 20 non-matching atom names) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 154954]: 16228 non-matching atom names atom names from topol.top will be used atom names from input.gro will be ignored
Compare the order of atoms in input.gro versus the [moleculetype] definition in the topology. Adding another entity shouldn’t have changed anything about the atom order but you haven’t provided us any detail about what you’ve actually done, so there is nothing more I can possibly suggest at this point.
How can I give you more information because it is not possible to send gro file here.